Rossi set a time of 1:55.362 as he ensured his world title defence will begin from the front row of the grid in Losail.
His Fiat Yamaha team-mate Lorenzo, who suffered a hand injury in pre-season, put in a strong performance with the Spaniard just over half a second off Stoner?s pace.
De Puniet heads the second row after a best time of 1:55.831. Loris Capirossi, on a Suzuki, will start a record-breaking 300th Grand Prix from fifth place.
The veteran, with a time of 1:55.899, was ahead of fellow Italian Andrea Dovizioso on a Honda.
Source: AFP Global Edition