But in a damp second practice Hamilton trailed in ninth, well behind Massa who was second to Fernando Alonso.
Schumacher, who has ended a three-year retirement to drive for Ross Brawn's new Mercedes team, was third quickest behind Massa and BMW Sauber's new signing Pedro De La Rosa.
Britain's Hamilton, who gone into the race off the back of wins at Silverstone and Hockenheim, was in second place behind Massa, but failing to make a real impression, when he punctured.
Coming from behind, Massa has it all to do, whereas Hamilton can play the percentages.
His mark soon disappears though as right behind him, Massa posts 1:29.329 to take pole in Turkey for the second straight year.
BBC: SPORT | Motorsport | Formula One | Turkish GP qualifying as it happened
The Englishman was demoted to third place behind Ferrari's Felipe Massa and BMW Sauber's Nick Heidfeld.
Massa was back behind the wheel of a Formula One car in a public session for the first time since his accident in Hungary in July, which left him needing life-saving skull surgery.
Fernando Alonso produced a stunning lap to grab pole, while team-mate Felipe Massa qualified third fastest behind 2009 champion Jenson Button's McLaren.
Hamilton had arrived in Japan determined to put his clash with Felipe Massa's Ferrari in Singapore behind him - instead the pair tangled again, touching through the 190mph 130R corner.
With team-mate Felipe Massa qualifying third, half a second behind Alonso and pole-sitter Sebastian Vettel, and ahead of the German's Red Bull team-mate Mark Webber, it was Ferrari's best qualifying result of the season so far.
"I would much rather arrive here seven points ahead, not behind, but I am very optimistic, " said Massa.
In the other, seven points behind his rival in the standings, is Ferrari's Felipe Massa.
Hamilton finished third behind Fernando Alonso and Nico Rosberg to open up a seven-point lead over Massa with just three rounds remaining.
Behind them, the second row has a similar red and silver theme, with Massa's team-mate Kimi Raikkonen ahead of Alonso's McLaren partner Lewis Hamilton.
Massa was happy to finish sixth, ahead of Vettel and Button but behind Red Bull's Mark Webber, fourth-placed Sergio Perez of McLaren and third-placed Romain Grosjean of Lotus.
Felipe Massa had been lightning quick in Friday's practice sessions but he was delayed behind traffic on his last lap and lines up in second.
Ferrari's Felipe Massa will start Sunday's race in third place, with Mercedes' Michael Schumacher a place behind the Brazilian.
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