The Virtuosi driver was sixth after the first runs, with Juri Vips, who also topped practice for Hitech, leading the field.
Doohan then improved to fourth, before his third run, a 1m31.965s took him to the top of the timesheet as the quickest lap of the day so far.
As the field emerged on fresh tyres, DAMS driver Ayumu Iwasa was next to take provisional pole, 0.04s faster than Doohan.
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