Dovizioso and Lorenzo maintained their qualifying one-two early in the race, however Bautista - who started sixth on the grid, but dropped to 12th on lap one - had reeled them in by lap 14 of 26.
Bautista then blasted past both fellow Aprilia rider Lorenzo and Honda star Dovizioso on the very same lap, with runaway championship leader Lorenzo soon dropping off the pace. Dovi hung in longer, but Bautista was simply too strong and eventually took victory by 4.367secs, with Lorenzo 1.781secs further back in third.
Dovizioso's second place moved him back into second in the championship, after his Misano misery, but Lorenzo leads by 51 points with just four rounds to go.
Thomas Luthi won a close battle with Hector Barbera and Alex de Angelis for fourth place. De Angelis is expected to soon confirm that he will join Lorenzo and Dovizioso in MotoGP next year.
Race results – Estoril:
1. Bautista (Aprilia)
2. Dovizioso (Honda) +4.367secs
3. Lorenzo (Aprilia) +6.148secs
4. Luthi (Aprilia) +12.685secs
5. Barbera (Aprilia) +13.411secs
6. de Angelis (Aprilia) +13.440secs
7. Simoncelli (Gilera) +13.322secs
8. Simon (Honda) +13.634secs
9. Lai (Aprilia) +1min 12.253secs
10. Abraham (Aprilia) +1min 12.319secs
14. Laverty (Honda) +1min 30.978secs
24. Linfoot (Aprilia) DNF