The rookie driver prised an opening over Guenther in the first sector, getting just under half a tenth ahead, but was able to extend his advantage - and Fenestraz's eventual 1m07.848s was far too much for the German driver to beat.
Despite showing great speed throughout the weekend and having headed FP2, Nick Cassidy had been brushed aside in the semifinals by Fenestraz by just over a tenth, as the Franco-Argentine booked his first finals appearance.
He was joined by Guenther, who was able to capitalise on Evans' brush with the wall to overturn the New Zealander's advantage in the first sector to set up a surprise final billing - and ensuring that Formula E would have a new polesitter in Cape Town.
Fenestraz also had to dispatch countryman Jean-Eric Vergne, having moved ahead by the first sector and continuing to build an advantage. Although the Nissan driver had shed some time following a slide at the end of the lap, he kept the Hyderabad winner at bay to move into the next round of duels.
Championship leader Pascal Wehrlein was drawn against Cassidy, but the Kiwi proved too strong for the Porsche ace and stamped his card for a semifinals appearance.
Evans and Sebastien Buemi were neck-and-neck after the opening sector, separated by just 0.001s, but the Swiss then locked up at the end of the waterfront stretch and nibbled the barrier, which stopped his progress and snapped the Envision's front wing.
An all-German quarterfinal between Guenther and Rene Rast, with the Maserati MSG driver's efforts in the opening pair of sectors proving enough to ensure Rast would be unable to progress any further.
On the grid, Cassidy starts ahead of Evans in an all-Kiwi second row, while Vergne will begin the race ahead of Wehrlein in fifth.
Following Rast's penalty carried over from his incident with Jake Dennis in Hyderabad, Buemi is elevated to seventh on the grid ahead of Dan Ticktum in eighth.
Antonio Felix da Costa was knocked out of Group A's top four at the session's final moment, as Fenestraz's headliner among the opening 11 drivers shuffled the Portuguese out of the progression zone.
Da Costa was unable to improve, and was leapfrogged by Ticktum and Norman Nato - who were both unable to displace Jean-Eric Vergne from the top four.
Jake Hughes also failed to progress into the duels, having scraped the wall earlier on in the session and was left relatively unsettled throughout the remainder of the 12-minute runtime.
Nico Muller did not leave the garage during Group A qualifying, as none of the Mahindra-powered cars took to the track; Abt team-mate Kelvin van der Linde and Mahindra pair Oliver Rowland and Lucas di Grassi were also confined to the garage in Group B.
Mahindra have henceforth withdrawn all four cars due to rear suspension issues, and this left just eight cars to contest for the four duels places.
As soon as Rast had punched in a time to move into the top of the session, it was red flagged as Mortara crashed at Turn 9 in a near carbon-copy of Buemi's Friday practice crash.
Sam Bird then followed the Swiss driver into the wall, with no apparent visible yellow or red flags heading into the blind, high-speed left-hander.
This brought the session to an end, with Bird having no opportunity to respond after being knocked out of the top four by Rast.