The Ducati Marlboro star was a huge 0.828secs clear of the opposition on Tuesday, then found another quarter of a second during Wednesday, pushing the 22-year-old 0.7secs under the official lap record and keeping him 0.339secs clear of nearest rival Nicky Hayden.
"We found something extra during these tests," warned Stoner. "Straight away yesterday, second lap out, we went a lot quicker than we did in the race on Sunday and we just kept going from there. Today we kept getting faster and faster. We weren't really trying to do that, we had a lot of tyres and things to test, so we weren't out there trying to do lap times, but everything just seemed to come to us quite easily.
"It's been a fantastic season for us and it's really good to end this test with some positives and some more information which the Ducati technicians can take back to Bologna, knowing that we've got something more to work with and knowing the right direction in which to head," added the ten times 2007 race winner.
Randy de Puniet was third fastest on his Honda debut, while Stoner's new team-mate Marco Melandri was 13th out of the 17 riders.