Sebastian Vettel was fastest in the second practice session as Webber completed a Red Bull one-two. The team looked unbeatable in the dry conditions, while Ferrari drivers Alonso and Massa finished fourth and fifth.
Jenson Button followed them in sixth, while Lewis Hamilton recovered from crashing for the third weekend in a row to set the 13th-fastest time of the session.
Friday practice at Suzuka was a chance to test parts, simply because on Saturday the track is set to be attacked by storms.
The dry day that was experienced today is likely to be unimportant in the context of the weekend, as the sessions are supposedly going to be very wet.
Jaime Alguersuari, Jarno Trulli, and Sakon Yamamoto got the first practice session under way, as all the drivers set installation laps.
After a large amount of anticipation for the first timed lap of the session, Yamamoto set the first fastest time, which was 1:42.950, with 27 minutes gone.
He narrowly beat that time by just over one second a minute later, before Belgian test driver Jérôme d'Ambrosio set the second fastest lap for Virgin Racing with an hour to go. Hulkenberg then beat the time by over five seconds to temporarily head to the top of the time sheets.
Local favourite Kamui Kobayashi, who sold over 1,000 tickets for the Kamui Kobayashi stand at the track, beat Hulkenberg's time by 0.1 seconds, while Buemi set the third fastest time and Senna set the slowest time of the session. Kobayashi then extended his lead over Hulkenberg in second.
Vitaly Petrov set the fifth fastest time on his first flying lap, before being beaten by d'Ambrosio and Trulli. However, he fought back to fourth place, while Massa set his first fastest lap with 53 minutes to go, sending him into fourth place.
Hulkenberg then set the fastest time from Kobayashi, who slid off the track at Degner.
Barrichello and Kovalainen joined the people setting times in sixth and ninth place respectively. Schumacher then set the second fastest time, before Alguersuari set the ninth fastest time.
Webber set his first lap and moved into 14th position. Lewis Hamilton went fastest, while Massa went sixth and Buemi went into ninth.
Rosberg set the slowest time, before Webber moved up to eighth and Schumacher went back up to third. Alguersuari moved to 11th position and Liuzzi went to 14th, while Barrichello moved to second and Heidfeld went to 10th. Vettel moved to sixth with almost half of the session remaining.
The flying laps were halted as yellow flags came out around the difficult Degner corners to notify everyone that Lewis Hamilton's car had stopped on the track after going onto the kerb and brushing a barrier, taking the wheel and part of the front wing off.
Hamilton was alright and got out of the car and briefly hung around before going back into the pit lane.
Hamilton had an extensive test session planned for new improvements, but he had to sit out the rest of the session and miss the first part of the second session later in the afternoon. Due to the rain forecast, he is not likely to be too far behind the others tomorrow.
He had set the fastest first sector time, with Vettel setting the second fastest time and Kubica setting the third fastest time. Alonso moved up to 15th and Sutil got up to eighth position.
Heidfeld, competing in his second race this season, went to fifth postion, but Vettel was fastest overall with Sutil moving to second after he set the fastest second sector time. Kubica moved up to second a few minutes later.
Red Bull continued to show their dominance, as championship leader Mark Webber set the second fastest time, while his teammate Vettel improved on his fastest time to have a greater lead at the top.
While Vettel and Webber continued with their dominance, several drivers switched places beneath them, and with ten minutes to go, Kubica, Sutil, and Hamilton were the other members of the top five.
Barrichello moved to sixth with his teammate in seventh. Schumacher ended the session in eighth position, with Heidfeld ninth and Rosberg 10th.
Massa was 11th, with Button, Alonso, Kobayashi, Petrov, Liuzzi, Buemi, and Alguersuari following for the established teams.
Kovalainen set the fastest time from the new team drivers, followed by Timo Glock, Jarno Trulli, d'Ambrosio, Senna, and Yamamoto in last place.
The second practice session got under way with many drivers setting installation laps. Kobayashi almost made a mistake as he went across the grass in the Esses, but did not crash and continued on his lap.
Alguersuari was in top position with Force India driver Vitantonio Liuzzi was second and Kobayashi in third, before Sutil went fastest and Heidfeld was second, while Buemi, Hulkenberg, Kubica, Kovalainen, Petrov, Senna, di Grassi and Yamamoto made up the rest of the timed laps.
After Button and Kubica had both moved up to top spot, Fernando Alonso went fastest with seven minutes of the session gone, followed by Vitaly Petrov and Nico Hulkenberg in third. However, Schumacher soon moved up to second after 11 minutes.
Webber set a lap which saw him go to third, before he set the fastest time, with his teammate Sebastian Vettel in third, before the German went fastest.
Kubica went into the gravel at turn 7, before slowly going back to the pits with a little bit of damage to his car.
Petrov, Alonso, Schumacher, Massa, Kubica, Hulkenberg, Button, and Barrichello were the other drivers in the top 10 aside from the Red Bull duo at the top. Sutil moved up to fourth, while his teammate Liuzzi was floundering down in 15th position.
Toro Rosso driver Sebastien Buemi spun into the gravel, but managed to get back on track. Massa then went into third place for Ferrari, before Mark Webber went fastest again, before Vettel took the place by just over 0.1 seconds.
Michael Schumacher went very wide and almost collided with the tyre barrier at Degner, but managed to avoid it. Lewis Hamilton then emerged for the final seven minutes, and was very slow and took 18th place.
As the session ended, Vettel remained in the top spot, followed by Webber, Kubica, Alonso, Massa, Button, Petrov, Schumacher, Sutil and Hulkenberg in the top 10.
The top driver outside the top 10 was Nico Rosberg, followed by Kobayashi, Hamilton, Barrichello, Heidfeld, Buemi, Alguersuari, Liuzzi, Kovalainen and Trulli, with di Grassi, Glock, Senna and Yamamoto making up the rest of the field.
Much as the results seem to suggest that the Red Bull team should win this race, the rain could make things pretty unpredictable!