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The Italian clocked a 2m06.733s to be the top Mahindra rider at 12th with teammate Jorge Martin slotting in at 14th 0.145s away.
Bagnaia has had a mixed run in Qatar after finishing fifth, 13th and 28th in the three practice session while Martin has gradually improved having finished 24th, 11th and ninth respectively.
But both riders haven't been able to get into the 2m05's against Mahindra's rivals Honda and KTM.
In an ultra competitive session under lights, the 19 riders ended within a second of KTM rider Romano Fenati, who took pole.
Among the other Mahindra-powered teams, the Peugeot branded rider Alexis Masbou was the next best at 21st followed by Platinum Bay's Karel Hanika at 23rd.
CIP's Tatsuki Suzuki was 25th followed by the other Platinum Bay rider Darryn Binder at 26th.
The last four positions were filled by John McPhee at 30th, Team Italia's Stefano Valtulini 31st, CIP's Fabio Spiranelli 32nd and Lorenzo Petrarca 33rd.
|Jorge Martin||Aspar Mahindra||2:06.733|
|Francesco Bagnaia||Aspar Mahindra||2:06.931|
|Darryn Binder||Platinum Bay||2:07.558|
|Karel Hanika||Platinum Bay||2:07.359|
|John McPhee||Peugeot SaxoPrint||2:07.847|
|Alexis Masbou||Peugeot SaxoPrint||2:07.209|
|Stefano Valtulini||Team Italia||2:08.336|
|Lorenzo Petrarca||Team Italia||2:10.433|
Qatar Moto3: Fenati takes first pole of new season
Qatar Moto3: Antonelli beats Binder by 0.007s in photo finish
|Location||Losail International Circuit|
|Drivers||Francesco Bagnaia , Karel Hanika , Jorge Martin , Darryn Binder , John McPhee , Tatsuki Suzuki , Alexis Masbou , Fabio Spiranelli , Livio Selva , Stefano Valtulini|
|Teams||CIP , Angel Nieto Team , Team Italia FMI|