Stoner, looking to complete a dream season with his eleventh victory on Sunday, was a full 0.68secs clear of the competition in morning practice before clipping a further 0.115secs off his best lap during the afternoon.
Although never toppled, the Ducati star's advantage nevertheless shrunk to just 0.116secs over Dunlop Yamaha Tech 3 rookie Sylvain Guintoli by the end of the day - aided by an unlimited tyre supply for the young Frenchman - with home hero Dani Pedrosa a close third for Repsol Honda.
Stoner's 2008 team-mate Marco Melandri had been the Australian's closet challenger in the first session, but dropped to fourth by the end of the afternoon to place him immediately ahead of Rizla Suzuki's Chris Vermeulen and Kawasaki's Randy de Puniet.
Alex Barros, riding in what looks like being his final race weekend after 21 years of world championship racing, had been a brave fourth in FP1 but suffered a technical problem at the start of the second session.
The Brazilian bounced back to claim seventh, while team-mate Chaz Davies had problems of a more physical kind; the 20-year-old suffered a heavy fall at the end of morning practice and was sent to hospital to have some back pain examined, forcing him to miss the afternoon session.
Valentino Rossi, starting what could well be his final MotoGP event with Michelin tyres, was left just behind Barros - and 0.652secs from Stoner - after a session in which he suffered two off-track excursions.
Nicky Hayden, who beat Rossi to claim the 2006 crown at Valencia one year ago, delivered some thrilling slides on his way to ninth, with fellow American John Hopkins tenth at the start of his final GSV-R weekend before joining Kawasaki.
Among those requiring most overnight progress are Colin Edwards and Loris Capirossi - Edwards was only 13th on his Fiat Yamaha, with Stoner's team-mate Capirossi one place behind.
Friday practice:1. Stoner
2. Guintoli
3. Pedrosa
4. Melandri
5. Vermeulen
6. de Puniet
7. Barros
8. Rossi
9. Hayden
10. Hopkins
11. Checa
12. Tamada
13. Edwards
14. Capirossi
15. Elias
16. Nakano
17. West
18. Davies
19. Roberts
