Leimer was in imperious form behind the wheel of his Racing Engineering machine, at one point holding pole position by 2.288 seconds.
His eventual margin was trimmed back to 0.915s, with nearest challenger Johnny Cecotto Jr overcoming a brief off at Village and his car coasting to a halt, before recovering to finish the session in second.
The session was red-flagged with 10 minutes remaining when iSport's Marcus Ericsson and Addax driver Cecotto simultaneously stopped out on the track. Ericsson required pushing off the circuit at Chapel, while Cecotto did not quite make it back to the pits under his own power.
Fortunately the marshals helped him, and his mechanics were able to refettle the car and send him back into battle.
Jolyon Palmer of iSport will start third, just 0.068s slower than Cecotto, and both will be hoping to avoid the collision they suffered in Valencia last time out.
Stefano Coletti grabbed fourth to cheer Scuderia Coloni's weekend, after the news of its exit from the series at the end of the season.
Lotus GP duo Esteban Gutierrez and James Calado will share the third row, the pairing just 0.016s apart on the timesheet.
Carlin's Rio Haryanto was seventh fastest, but he will start 17th due to a penalty for his clash with Calado in Valencia.
That moves team-mate Max Chilton up to seventh, ahead of title challenger Luiz Razia (Arden) and Caterham's Giedo van der Garde.
It was a bizarre session for DAMS, with both its drivers off the pace and stopping out on track within moments of each other.
Points leader Davide Valsecchi will start 11th, after pulling off at Club corner, while Felipe Nasr qualified one spot ahead of him, his car grinding to a halt on the Wellington Straight.