New Repsol Honda rider Casey Stoner, unbeaten at the previous Sepang MotoGP test, began the Qatar night test in a close second place behind team-mate Dani Pedrosa.
While Pedrosa is still to chose his race chassis, Stoner has now decided to use the standard 2011 design this season.
As a result, both Stoner's RCVs were fitted with that chassis and he tested different rider positions and race set-up during his 32 Sunday laps.
The Australian was 0.143sec slower than Pedrosa, but recorded 12 laps under 1min 57sec.
That compares with just two for Pedrosa and 13 for Yamaha's world champion Jorge Lorenzo, who was fifth fastest in terms of single lap pace.
"Everything has gone well with the bike and in general we don't have a whole lot to test here, we're just trying to get more out of the balance of the bike - both bikes have the same chassis but we tried very different riding positions,” confirmed Stoner.
“It seems to be more difficult to get a decent lap time on the harder tyres, having made my fastest time on an older soft tyre, but our consistency seems to be very good also with the hardest compound.
“We've been trying to get a little bit more grip and turning out of the bike and work on set-up for this circuit, focusing on race set-up.
“It's nice to be so close to the season and at the final test. I'm just pleased the team reached here safely and there were no casualties back in the HRC Headquarters in Saitama, my thoughts are with all the people in Japan.”
Third Repsol Honda rider Andrea Dovizioso, who has also chosen the standard 2011 chassis, was seventh fastest.
The last day of pre-season testing takes place on Monday.