The Imola feature race winner had been running in 13th place for Trident before setting a 1m33.516s to claim pole, just 0.07s quicker than the ART Grand Prix driver.
It continues his consistent run of qualifying so far this season, having qualified second at both Bahrain and Imola.
Alexander Smolyar will line up third for MP Motorsport, having topped the times earlier in the session before he was surpassed by Martins and then Stanek.
Hitech's Isack Hadjar was the first driver to set a representative flying lap, with a 1m34.181s to top the timesheet early on.
But he was soon pushed down the order by Caio Collet (MP Motorsport), who was quickest with a 1m34.026s, before Van Amersfoort Racing's Franco Colapinto and Martins also slotted in ahead of him.
The top 14 was running within just one second of the leader after the first runs, during which Stanek and William Alatalo (Jenzer Motorsport) took trips over the gravel at Turns 7 and 11 respectively.
Running resumed with 20 minutes left on the clock, with Hadjar briefly reclaiming the top spot before Ollie Bearman went fastest.
The Prema driver's time at the top was shortlived, with Smolyar next to claim provisional pole with a 1m33.613s.
Martins was next to take the lead, going just 0.05s quicker, while Arthur Leclerc (Prema) slotted into third, with Bearman in fourth.
The field emerged for their final runs with 10 minutes left on the clock, prompting heavy traffic at Banc Sabadell, with some drivers running three wide in a bid to be last across the line.
The final order had looked set as Martins, Smolyar and Hadjar before Stanek's last-minute attempt put him top of the timesheet.
Trident's Zane Maloney was disqualified from qualifying for failing to stop at the weighbridge.
He was set to line up on pole for Saturday's reverse-grid sprint race, with David Vidales (Campos Racing) alongside him and Juan Manuel Correa in third for ART, returning from a stress fracture in his left foot which caused him to miss the last round at Imola.
| Cla | Driver | Team | Laps | Time | Gap |
|---|---|---|---|---|---|
| 1 |  Roman Staněk |  Trident | 11 | 1'33.516 | |
| 2 |  Victor Martins | ART Grand Prix | 11 | 1'33.568 | 0.052 |
| 3 |  Alexander Smolyar |  MP Motorsport | 11 | 1'33.613 | 0.097 |
| 4 | Isack Hadjar |  HitechGP | 11 | 1'33.726 | 0.210 |
| 5 |  Arthur Leclerc | Prema Powerteam | 11 | 1'33.731 | 0.215 |
| 6 | Oliver Bearman | Prema Powerteam | 11 | 1'33.747 | 0.231 |
| 7 |  Caio Collet | MP Motorsport | 11 | 1'33.750 | 0.234 |
| 8 |  Kaylen Frederick | HitechGP | 11 | 1'33.805 | 0.289 |
| 9 | Jak Crawford | Prema Powerteam | 11 | 1'33.825 | 0.309 |
| 10 | Juan Manuel Correa | ART Grand Prix | 11 | 1'33.857 | 0.341 |
| 11 |  David Vidales | Campos Racing | 11 | 1'33.873 | 0.357 |
| 12 |  Zane Maloney | Trident | 10 | 1'33.926 | 0.410 |
| 13 |  Franco Colapinto | Van Amersfoort Racing | 10 | 1'33.963 | 0.447 |
| 14 |  Gregoire Saucy | ART Grand Prix | 11 | 1'34.040 | 0.524 |
| 15 |  Oliver Rasmussen | Trident | 11 | 1'34.041 | 0.525 |
| 16 | Pepe Martí | Campos Racing | 11 | 1'34.117 | 0.601 |
| 17 | Reece Ushijima | Van Amersfoort Racing | 11 | 1'34.180 | 0.664 |
| 18 |  Rafael Villagomez | Van Amersfoort Racing | 11 | 1'34.317 | 0.801 |
| 19 | Zak O'Sullivan | Carlin | 11 | 1'34.320 | 0.804 |
| 20 | Hunter Yeany | Campos Racing | 11 | 1'34.342 | 0.826 |
| 21 |  William Alatalo | Jenzer Motorsport | 10 | 1'34.568 | 1.052 |
| 22 |  Lirim Zendeli | Charouz Racing System | 11 | 1'34.686 | 1.170 |
| 23 |  Kush Maini | MP Motorsport | 11 | 1'34.735 | 1.219 |
| 24 |  Nazim Azman | HitechGP | 11 | 1'34.795 | 1.279 |
| 25 |  Ido Cohen | Jenzer Motorsport | 12 | 1'34.866 | 1.350 |
| 26 | Enzo Trulli | Carlin | 10 | 1'34.973 | 1.457 |
| 27 | Federico Malvestiti | Jenzer Motorsport | 10 | 1'35.096 | 1.580 |
| 28 | Brad Benavides | Carlin | 11 | 1'35.337 | 1.821 |
| 29 | Francesco Pizzi | Charouz Racing System | 11 | 1'35.549 | 2.033 |
| 30 |  László Tóth | Charouz Racing System | 11 | 1'35.575 | 2.059 |
| View full results | |||||
