Alonso finished in 4th, but Massa's drivethrough penalty affected his race finishing 10th.
Sebastian Vettel and Mark Webber swapped their starting places at the and of the race, finishing first and second respectively.
Both drivers had a solid start and drove a good race with a lot of midfield battles taking place.
Paul Di Resta finished in P11 ahead of Adrian Sutil in P14 in today's Japanese race
“Both drivers showed stout character today”
Felipe Massa done a lap of 1.31.378, while Fernando Alonso did it in 1.31.665.
P20 and P21 for Caterham by Charles Pic and Giedo van der Garde respectively for tomorrow's race start at Suzuka
Webber claimed his 12th career pole position with a time of 1m30.915s, ahead of his team mate Sebastian Vettel.
Romain Grosjean qualified P4 with team-mate Kimi Räikkönen P9 ahead of tomorrow’s Japanese Grand Prix.
Mark Webber posted the best time in today's qualifying at Suzuka while Sebastian Vettel suffered KERS issue but placed his RB9 2nd.
The session also saw unusually close gaps, with the top six in less than half a second and top 10 less than a second
Australian Red Bull driver Mark Webber grabs the Japanese Grand Prix pole
Vettel goes fastest on P Zero white medium
“This weekend has been overshadowed by tragedy”
Kimi Räikkönen set the fourth fastest and Romain Grosjean the fifth fastest time on the first day of practice for the Japanese Grand Prix.
A smooth Friday for Nico and learning a new track for Esteban.