Talmacsi, who is just one point ahead of the Spaniard heading into Sunday's Malaysian Grand Prix, had held a near one second advantage with three minutes to go - but Faubel, fifth at that stage, went on to produce an excellent final effort to pinch only his second pole of the season by 0.116secs.
Talmacsi didn't improve on his last lap, but remained comfortably clear of Sandro Cortese, while Pol Espargaro completed an all Aprilia front row. Simone Corsi heads row two, in front of KTM's Tommy Koyama and Derbi's Lukas Pesek.
Final qualifying – Sepang:1. Faubel (Aprilia)
2. Talmacsi (Aprilia) +0.116secs
3. Cortese (Aprilia) +0.814secs
4. Espargaro (Aprilia) +0.839secs
5. Corsi (Aprilia) +1.020secs
6. Koyama (KTM) +1.113secs
7. Pesek (Derbi) +1.303secs
8. Olive (Aprilia) +1.396secs
9. Nieto (Aprilia) +1.411secs
10. Pasini (Aprilia) +1.471secs
15. Smith (Honda) +2.308secs
25. Webb (Honda) +3.539secs