Ducati/Bridgestone test rider Niccolo Canepa was the second best Desmosedici rider in seventh place, with Tech 3 Yamaha's James Toseland eighth and Kawasaki test rider Olivier Jacque ninth.
Toseland's team-mate Colin Edwards concluded testing on Monday, while Jacque has been substituting for Kawasaki race rider John Hopkins, who withdrew from the test due to discomfort from a minor rib injury sustained during the grand prix weekend.
Marco Melandri, who says he will ride for Kawasaki next season, was tenth fastest on the second factory Ducati, with Antony West - whose ride he will take - rounding out the field with a best lap time over three seconds from Stoner, but less than one tenth from Melandri.
Round 13 of the 2008 MotoGP World Championship, the San Marino Grand Prix at Misano, takes place on August 31.
