Talmacsi and Mattia Pasini took an early lead in the 19 lap race, but were caught during the second half by Sergio Gadea, Lukas Pesek and Faubel.
With three laps to go Gadea fell from second position, allowing Pasini to pull a slight advantage, but that was erased by a later mistake and Faubel pounced for the lead soon after.
Talmacsi demoted Pasini a further position, then led the race with half a lap to go, but subsequently lost out to all three of his rivals to cross the line a disappointed fourth.
Faubel beat Pasini by just 0.070secs at the flag with home hero Pesek taking a well deserved third after a poor start left him tenth on the opening lap.
Faubel's victory means he now leads Talmacsi by 10 points in the world championship standings.
Race results – Brno:
1. Faubel (Aprilia)
2. Pasini (Aprilia) +0.070secs
3. Pesek (Derbi) +0.222secs
4. Talmacsi (Aprilia) +0.272secs
5. Koyama (KTM) +7.607secs
6. Espargaro (Aprilia) +12.066secs
7. Corsi (Aprilia) +12.394secs
8. Ranseder (Derbi) +13.003secs
9. Krummenacher (KTM) +19.764secs
10. Cortese (Aprilia) +24.043secs
13. Smith (Honda) +33.863secs
28. Webb (Honda) +1min 23.792secs
