Hughes had been fractionally faster than Fenestraz in the opening sector despite a slide through Sainte Devote, but the Briton initially threw away the chance of pole after cutting the Nouvelle Chicane.
Fenestraz posted a 1m29.131s which would have been enough for the top spot, but he was stripped of his lap time post-session after he was found to have exceeded the 350kW power limit during his final duel attempt.
Hughes will start this afternoon's race from pole despite also having his lap time cancelled due to going off track. This is because he was running ahead of Fenestraz for their final duel, as the driver who sets the faster semi-final time runs second under the current regulations.
Fenestraz had earlier set an incredible 1m28.773s – the fastest lap across qualifying – in his semi-final duel against team-mate Norman Nato, going faster in all three sectors to finish nearly half a second clear of the Frenchman.
Hughes had progressed to the final after also setting a time below the 1m29s mark, with a lap 0.508s clear of Maximilian Gunther.
NIO 333’s Sergio Sette Camara had comfortably beaten Gunther in the last quarter-final duel, but the Brazilian was stripped of his lap time having gone through a red light at the end of the pitlane.
Gunther’s Maserati MSG team-mate Edoardo Mortara lost out to Hughes in their quarter-final duel, the Briton having gone through with a time nearly four tenths faster.
Fenestraz had beaten NIO 333’s Dan Ticktum in his quarter-final bout, going quicker than the Briton in all three sectors to post a 1m29.031s – the quickest time in that segment of qualifying.
An incredible final sector by Nato meant he bested Jaguar’s Mitch Evans, a 1m29.113s almost three tenths quicker than the Kiwi having trailed him in the opening sector.
Gunther had earlier headed the second qualifying group with a 1m30.175s from Hughes and Mortara with Sette Camara fourth – just 0.095s covering the top four.
Envision Racing’s Nick Cassidy failed to progress having lost two tenths in the final sector after catching Gunther in the last corner – with the German under investigation – as fellow championship challenger Jake Dennis finishing behind the Kiwi in sixth.
Nissan claimed a surprise 1-2 in the opening qualifying group, Nato posting a 1m30.138s to go 0.011s faster than team-mate Fenestraz, with Ticktum just 0.007s further back in an incredibly tight session.
Evans secured the final duel spot, beating Andretti Autosport’s Andre Lotterer by less than half a tenth as championship leader Pascal Wehrlein once again struggled in qualifying, finishing sixth in the group and will start 11th for the race.
The Porsche driver was promoted a spot as Stoffel Vandoorne and DS Penske team-mate Jean-Eric Vergne were stripped of all their times due to a tyre pressure violation and will start on the back row.
Formula E - Monaco E-Prix starting grid
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