In Brazil, the Porsche driver initially took the lead in the opening sector, only to be overtaken by Vandoorne in the subsequent sectors.
Despite starting from pole position in Sao Paulo last year, the DS Penske racer fell short of securing the top spot by a mere 0.002 seconds.
Wehrlein advanced to the finals after defeating Maximilian Guenther by nearly three-tenths, following a momentary slip by the Maserati MSG driver at Turn 18.
However, due to changes in both his gearbox and inverter before qualifying, the German incurred a 40-place grid penalty and will start from the back of the grid.
An error in the first sector cost Jean-Eric Vergne three-tenths in an intra-team battle with Vandoorne, who ultimately set the fastest lap time of the qualifying session with a 1m12.566s.
Wehrlein comfortably secured his spot in the semi-final with the fastest time across all three sectors, posting a 1m12.846s and knocking out Edoardo Mortara.
Similarly, Guenther advanced by defeating McLaren’s Sam Bird, while Mitch Evans lost two-tenths to Vandoorne after running deep into Turn 1, resulting in a gap of 0.156s at the end of the lap.
Vergne received a free pass in his quarter-final after Nico Muller damaged his Abt machine’s right-front suspension, preventing him from advancing to the next stage.
The first qualifying group was briefly halted by a red flag when debris, suspected to be a weather balloon, landed on the track between Turns 6-7.
Once the track was cleared, championship leader Nick Cassidy narrowly missed out on a spot in the duels by just 0.011s at the finish line.
Following Cassidy were Oliver Rowland (Nissan), Nyck de Vries (Mahindra), Lucas di Grassi (Abt), Robin Frijns (Envision), Sergio Sette Camara (ERT), and Norman Nato (Andretti).
In terms of timings, Vergne led a DS Penske 1-2 with a 1m13.731s, followed by Evans and Muller in the top four.
The second qualifying group saw four different powertrain manufacturers occupying top positions, with Guenther leading the pack with a time of 1m13.516s, ahead of Wehrlein, Mortara, and Bird.
Antonio Felix da Costa of Porsche narrowly missed out on a spot in the duels by 0.005s, while reigning Formula E champion Jake Dennis trailed just half a tenth behind.
The second McLaren entry, Jake Hughes, led the rest of the group, including Sacha Fenestraz (Nissan), Jehan Daruvala (Maserati MSG), Sebastien Buemi (Envision), and Dan Ticktum (ERT).