The Swiss-Italian posted a 1m01.741s, the fastest time from the entirety of qualifying, in his final qualifying duel to register his and Mahindra’s first points of the season having endured a difficult campaign so far.
Mortara was only 0.011s quicker than Vandoorne in the opening sector of their final duel, but a less than ideal exit from the Turn 7 hairpin for the DS Penske driver meant he lost two tenths.
The margin at the line was 0.267s in Mortara’s favour, having last taken pole two years ago, also at the Tempelhof Airport circuit in Berlin but on a different layout.
Vandoorne’s 1m01.844s allowed him to beat ERT’s Sergio Sette Camara by 0.167s in their semi-final duel, while Mortara recovered from a fractionally slower opening sector to beat the second DS Penske of Jean-Eric Vergne by a tenth.
Championship leader and Porsche driver Pascal Wehrlein lost out in his quarter-final duel against Vergne by only 0.082s, while Vandoorne progressed at the expense of Maserati MSG’s Maximilian Guenther by more than two tenths.
The second Maserati of Jehan Daruvala, who faces a 20-place grid penalty after the gearbox in his car was replaced overnight, also failed by more than two tenths in his duel against Mortara.
Abt’s Lucas di Grassi made it through to the duels for the first time this season but fell short by 0.229s against Sette Camara.
Despite brushing the wall at the final corner in the opening qualifying group, Mortara topped the session with a 1m02.619s and was joined by Wehrlein, Vergne and Daruvala in the duels.
The second Porsche of Antonio Felix da Costa missed out on progressing by 0.084s as he finished ahead of Monaco winner and Jaguar driver, Mitch Evans.
Also eliminated were Dan Ticktum (ERT), Mahindra’s Jordan King ahead of his Formula E debut and Sacha Fenestraz (Nissan).
Joel Eriksson, replacing Robin Frijns at Envision this weekend, finished 10th ahead of reigning champion Jake Dennis, the Andretti driver last but less than half a second slower than Mortara’s best.
Dennis’s team-mate Norman Nato fared little better in the second qualifying group as he also finished last to complete a disastrous session for the American team.
Di Grassi had topped the group, setting a 1m02.615s with his final effort to head Guenther, who like Mortara also brushed the wall at the final turn, Vandoorne and Sette Camara.
Championship protagonist Nick Cassidy failed to advance by 0.079s and was joined by the second Abt of Kelvin van der Linde, replacing Nico Muller, and Taylor Barnard in for the injured Sam Bird again.
Nissan’s Oliver Rowland finished eighth ahead of the second McLaren of Jake Hughes, while Formula E debutant Paul Aron was 10th for Envision and less than half a second behind di Grassi.
Berlin E-Prix - Qualifying results:
| Cla | Nº | Driver | Car / Engine | Time | Gap |
| 1 | 48 | Edoardo Mortara | Mahindra | 1'01.741 | - |
| 2 | 2 | S.Vandoorne | DS | 1'02.008 | 0.267 |
| 3 | 25 | Jean-Éric Vergne | DS | 1'01.959 | 0.218 |
| 4 | 3 | S.Sette Câmara | ERT | 1'02.031 | 0.290 |
| 5 | 7 | Max Günther | Maserati | 1'02.156 | 0.415 |
| 6 | 94 | Pascal Wehrlein | Porsche | 1'02.294 | 0.553 |
| 7 | 11 | Lucas di Grassi | Mahindra | 1'02.388 | 0.647 |
| 8 | 13 | A.F.da Costa | Porsche | 1'02.885 | 1.144 |
| 9 | 37 | Nick Cassidy | Jaguar | 1'02.840 | 1.099 |
| 10 | 9 | Mitch Evans | Jaguar | 1'02.893 | 1.152 |
| 11 | 51 | K.van der Linde | Mahindra | 1'02.870 | 1.129 |
| 12 | 33 | Dan Ticktum | ERT | 1'02.943 | 1.202 |
| 13 | 8 | Taylor Barnard | Nissan | 1'02.926 | 1.185 |
| 14 | 21 | Jordan King | Mahindra | 1'02.954 | 1.213 |
| 15 | 22 | Oliver Rowland | Nissan | 1'02.948 | 1.207 |
| 16 | 23 | Sacha Fenestraz | Nissan | 1'03.093 | 1.352 |
| 17 | 5 | Jake Hughes | Nissan | 1'03.037 | 1.296 |
| 18 | 4 | Joel Eriksson | Jaguar | 1'03.094 | 1.353 |
| 19 | 16 | Paul Aron | Jaguar | 1'03.092 | 1.351 |
| 20 | 1 | Jake Dennis | Porsche | 1'03.110 | 1.369 |
| 21 | 17 | Norman Nato | Porsche | 1'03.159 | 1.418 |
| 22 | 18 | Jehan Daruvala | Maserati | 1'02.332 | 0.591 |
