Massa qualified on pole position for his home race at Interlagos while Schumacher, retiring after the season-ending title-decider, starts 10th.
The German must win to have any hope of an eighth championship while Renault's Fernando Alonso, who qualified fourth, needs just one point.
"Of course I am disappointed but these things can happen," declared Schumacher.
"Sure, it's a big handicap starting from 10th place. The only good part of today is that Felipe is on pole which must be very satisfying for him here at his home race. I hope that tomorrow he can win the race."
Massa, wearing a race suit in the Brazilian colours, said the third pole of his career and first in Brazil was a dream come true.
"Tomorrow I will do my utmost to win," he said. "I know it will be a tough race but everything is in place for me to achieve that goal.
"I am sorry for Michael who was really unlucky...but I still believe we can get both our cars ahead of the others, which is vital if we are to win the constructors' championship."
Ferrari are nine points adrift of Renault, who have both Alonso and Italian Giancarlo Fisichella ahead of Schumacher.
Ferrari technical director Ross Brawn said anything was possible.
"We could still pull off a one-two tomorrow," he said in a team release. "The cars are performing strongly, the Bridgestone tyres mean we can do consistent lap times and the weather forecast for slightly higher temperatures should all work in our favour.
"And let's not forget that in the past, Michael has managed to win races starting even further back on the grid."
