John Hopkins took an encouraging seventh for Kawasaki, just ahead of another injured rider, Repsol Honda's Dani Pedrosa, who used a softer tyre at the end of the session to cut his lap time.
Seven times world champion Valentino Rossi was ninth - and complaining about the cold temperatures - with former factory team-mate Colin Edwards tenth (and 1.4secs behind Stoner) on the second Tech 3 M1.
2006 world champion Nicky Hayden was just twelfth fastest, while Rizla Suzuki riders Chris Vermeulen and Loris Capirossi again struggled - the pair being left 14th and 15th on day one, just in front of Stoner's beleaguered team-mate Marco Melandri.
Anthony West was the session's only crasher, the Kawasaki rider escaping from a big accident early on, whilst the majority of the feedback from the teams and riders with regard to track visibility and riding conditions was highly positive.
The two-night Qatar test concludes in the early hours of Saturday morning, after which the MotoGP riders will be in action for real during the season-opening Qatar Grand Prix from March 7-9 - MotoGP's first ever night race.
