The remaining top ten position were occupied by JiR Team Scot rookie Andrea Dovizioso, Hayden, Rizla Suzuki's Chris Vermeulen, San Carlo Honda Gresini rookie Alex de Angelis and then five-times MotoGP world champion Valentino Rossi - who ended the test 1.7secs slower than his Michelin-shod team-mate Lorenzo and with work clearly still to do.
It definitely wasn't the end to the pre-season that the Italian had been hoping for, especially after two promising tests, and Rossi later revealed that they'd run out of time after heading in the wrong direction with tyre choice for the cool conditions.
The session was briefly red-flagged at around 9.30pm local time following a fall by new Rizla Suzuki Loris Capirossi at turn seven, but the veteran Italian was unhurt and once the action resumed he was soon back out riding again - eventually lapping eleventh fastest.
In addition to the tumbles by former team-mates Stoner and Capirossi, there were crashes late in the session for Capirossi's troubled Ducati replacement Marco Melandri, San Carlo Honda Gresini's Shinya Nakano and Alice Team's Sylvain Guintoli - the chilly 13°C track temperature a likely factor in those falls.
Guintoli's bike was badly damaged, but he was later given the all clear by doctors.
The opening pair of practice sessions for the 2008 Qatar Grand Prix will take place on March 7.