The 43-year-old was almost two seconds slower than Hamilton's leading time of 1:12.458, finishing behind the Englishman's replacement at McLaren next year -- Sergio Perez of Sauber.
"I am not particularly happy about the qualifying session," Schumacher said.
"We might have compromised the car too much for the rain which is expected for tomorrow and was also forecast for qualifying.
"My starting position is now quite tricky, and I will have to see what we can make out of it.
Sauber's new signing Nico Hulkenberg will start sixth in his final race for Force India at a track where the German claimed a surprise pole position in 2010.
Former world champion Kimi Raikkonen, seeking to hold off Hamilton for third place in the drivers' standings, will be eighth on the grid ahead of Mercedes' Nico Rosberg and Force India's Paul di Resta.
Bruno Senna will start 11th as he seeks to earn a new deal with Williams at the circuit where his three-time world champion uncle Ayrton made his name as a Brazilian folk hero.