Schumacher was the quickest, 0.172 seconds ahead of champion Alonso, on a damp track after morning drizzle at an overcast circuit.
The seven-times world champion lags the 25-year-old Spaniard by two points with two races remaining after Sunday's showdown in Shanghai.
Briton Jenson Button, a first time winner for Honda in Hungary last month, followed the title contenders with the third best time.
The two V10-powered Toro Rossos of Italian Vitantonio Liuzzi and American Scott Speed were a surprising fourth and fifth.
McLaren's Kimi Raikkonen, Schumacher's replacement at Ferrari next year, spun twice towards the end of the session and failed to set a timed lap.
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1. Michael Schumacher (Germany) Ferrari 1:40.193
2. Fernando Alonso (Spain) Renault 1:40.365
3. Jenson Button (Britain) Honda 1:40.590
4. Vitantonio Liuzzi (Italy) Toro Rosso - Cosworth 1:40.795
5. Scott Speed (U.S.) Toro Rosso - Cosworth 1:41.150
6. Mark Webber (Australia) Williams - Cosworth 1:41.287
7. Christijan Albers (Netherlands) MF1 - Toyota 1:41.463
8. Giancarlo Fisichella (Italy) Renault 1:41.691
9. Pedro de la Rosa (Spain) McLaren 1:41.823
10. David Coulthard (Britain) RedBull - Ferrari 1:41.836
11. Nico Rosberg (Germany) Williams - Cosworth 1:42.588
12. Tiago Monteiro (Portugal) MF1 - Toyota 1:42.612
13. Nick Heidfeld (Germany) BMW Sauber 1:43.216
14. Rubens Barrichello (Brazil) Honda 1:43.448
15. Felipe Massa (Brazil) Ferrari 1:43.500
16. Takuma Sato (Japan) Super Aguri - Honda 1:43.722
17. Jarno Trulli (Italy) Toyota 1:44.027
18. Robert Doornbos (Netherlands) RedBull - Ferrari 1:45.434
19. Ralf Schumacher (Germany) Toyota 1:46.023
20. Sakon Yamamoto (Japan) Super Aguri - Honda 1:46.850
nc. Robert Kubica (Poland) BMW Sauber
nc. Kimi Raikkonen (Finland) McLaren
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