Newly-crowned champion Jenson Button also drilled in a series of personal bests to end P2 in third place, ahead of Sebastien Vettel in the Red Bull.
The second practice in Abu Dhabi began under twilight to replicate the conditions drivers will experience in Sundays grand prix.
Ten minutes into the session, 19 of the 20 runners had completed timed laps, but it was the both McLarens, Button in the Brawn and Sebastien Buemi in the first of the Toro Rossos who found themselves at the top of the times.
Kubica was the first to record a representative time by matching Hamiltons 1m43.9 on only his first run of the session, indicating there was far more pace to be found.
Kubica didnt hold on to the top spot for long as Hamilton produced consistently quick times and was the first to enter the 1m42s with a time a whole second quicker than his fastest in P1.
The 2008 world champion improved again to a 1m42.7, however, a storming lap from Buemi, put him back at the head of the leaderboard and six tenths ahead of Hamilton just 15 minutes into the session.
At this point, Vettel and both Ferraris were at the tail of the timesheets having completed relatively short runs.
Mark Webber in the second Red Bull became the first to try the softer, option tyres and he slotted into seventh place with a 1m43.3, although he quickly improved to fourth on his next attempt.
Times kept improving, although nobody was able to beat Buemis time until Hamilton drilled in a time of 1m41.564 to go quickest.
Vettel then tried to beat Hamilton and, despite being up at sector two by two hundredths of a second, the young German lost two tenths in the final sector of the lap and could only manage the second quickest time.
Buemi then recorded a 1m41.6 to move into second ahead of Vettel, but Kovalainen in the second McLaren who was less than a tenth off Hamiltons fastest lap time soon beat him.
At around half-distance Kubica suffered an engine failure and was no longer able to continue in the session.
The BMW Sauber engine had completed a lot of miles, but because Kubic was on the limit of his yearly engine allocation, he will be handed a grid penalty for Sundays race.
Raikkonen was able to put his Ferrari in the top ten, recording the sixth quickest time ahead of Button and directly behind Vettel.
His team-mate Giancarlo Fisichella then managed to get himself off the bottom of the timesheets with the 11th fastest time, however, he was shuffled down the order by quick times from Nico Rosberg, Nick Heidfeld and Kamui Kobayashi.
With half an hour to go in the session drivers were not able to make significant improvements, although the Red Bull pairing took small chunks out of their times, Vettel slotting into second and Webber in fifth.
At this point, with Hamilton in the lead, Kovalainen had been knocked down to third by Vettel and Buemi to fourth and the two Brawns were in sixth and seventh.
But, with less than 20 minutes to go, Hamilton upped the pace again by six hundredths of a second with a 1m41.504.
Shortly after, Kobayashi was able to put his Toyota in third in the times with a 1m41.6, whereas his more experienced team-mate Jarno Trulli was down in 12th and unable to improve.
Button jumped up to fifth fastest on his final run of the session and he continued to put in personal bests to go further up the leaderboard to go second fastest.
Vettel got back into third on his last run of Friday practice, but he was moved down to fourth by a lightening quick lap of 1m41.3 from Kovalainen, putting the Finn at the head of the times ahead of Hamilton.
The second practice in Abu Dhabi began under twilight to replicate the conditions drivers will experience in Sundays grand prix.
Ten minutes into the session, 19 of the 20 runners had completed timed laps, but it was the both McLarens, Button in the Brawn and Sebastien Buemi in the first of the Toro Rossos who found themselves at the top of the times.
Kubica was the first to record a representative time by matching Hamiltons 1m43.9 on only his first run of the session, indicating there was far more pace to be found.
Kubica didnt hold on to the top spot for long as Hamilton produced consistently quick times and was the first to enter the 1m42s with a time a whole second quicker than his fastest in P1.
The 2008 world champion improved again to a 1m42.7, however, a storming lap from Buemi, put him back at the head of the leaderboard and six tenths ahead of Hamilton just 15 minutes into the session.
At this point, Vettel and both Ferraris were at the tail of the timesheets having completed relatively short runs.
Mark Webber in the second Red Bull became the first to try the softer, option tyres and he slotted into seventh place with a 1m43.3, although he quickly improved to fourth on his next attempt.
Times kept improving, although nobody was able to beat Buemis time until Hamilton drilled in a time of 1m41.564 to go quickest.
Vettel then tried to beat Hamilton and, despite being up at sector two by two hundredths of a second, the young German lost two tenths in the final sector of the lap and could only manage the second quickest time.
Buemi then recorded a 1m41.6 to move into second ahead of Vettel, but Kovalainen in the second McLaren who was less than a tenth off Hamiltons fastest lap time soon beat him.
At around half-distance Kubica suffered an engine failure and was no longer able to continue in the session.
The BMW Sauber engine had completed a lot of miles, but because Kubic was on the limit of his yearly engine allocation, he will be handed a grid penalty for Sundays race.
Raikkonen was able to put his Ferrari in the top ten, recording the sixth quickest time ahead of Button and directly behind Vettel.
His team-mate Giancarlo Fisichella then managed to get himself off the bottom of the timesheets with the 11th fastest time, however, he was shuffled down the order by quick times from Nico Rosberg, Nick Heidfeld and Kamui Kobayashi.
With half an hour to go in the session drivers were not able to make significant improvements, although the Red Bull pairing took small chunks out of their times, Vettel slotting into second and Webber in fifth.
At this point, with Hamilton in the lead, Kovalainen had been knocked down to third by Vettel and Buemi to fourth and the two Brawns were in sixth and seventh.
But, with less than 20 minutes to go, Hamilton upped the pace again by six hundredths of a second with a 1m41.504.
Shortly after, Kobayashi was able to put his Toyota in third in the times with a 1m41.6, whereas his more experienced team-mate Jarno Trulli was down in 12th and unable to improve.
Button jumped up to fifth fastest on his final run of the session and he continued to put in personal bests to go further up the leaderboard to go second fastest.
Vettel got back into third on his last run of Friday practice, but he was moved down to fourth by a lightening quick lap of 1m41.3 from Kovalainen, putting the Finn at the head of the times ahead of Hamilton.
