German racer leads from Mihai Marienscu and Alex Fontana
On a now dry track following the morning's rain, the 21-year-old German set a best lap of 1:33.811s early on and couldn't be bettered with Swiss teenager Mathéo Tuscher in fourth and practice one pace-setter Luciano Bacheta in fifth.
In the first part of the 45-minute session it was British driver Bacheta who laid down the early benchmark lapping in the 1:34s ahead of Chinese racer David Zhu, Kevin Mirocha and Daniel McKenzie.
Tuscher then went top shortly after the halfway point before Fontana and then Pommer eclipsed the 15-year-old with Marinescu, currently lying second in the championship, moved into P2.
With five minutes to go and now on a completely dry track, the front runners were able to match the times set during yesterday's final test session with Pommer the first and only driver to break into the 1:33s and going 0.224s ahead of his nearest rival.
Indian racer Parthiva Sureshwaren impressed to finish in sixth for the session ahead of Zhu and 2011 F2 runner-up Christopher Zanella who was off his usual quick pace.
McKenzie ended ninth with Pole Mirocha completing the top 10 driver which were separated by just over a second.
Saturday's opening qualifying session gets underway at 09:15 (local time) with full coverage, including live timing, on the F2 website formulatwo.com.
F2 Results: Portugal Free Practice 2:
1. Markus Pommer, 1:33.811s2. Mihai Marinescu, +0.224s 3. Alex Fontana, +0.433s 4. Mathéo Tuscher, +0.531s 5. Luciano Bacheta, +0.576s 6. Parthiva Sureshwaren, +0.738s7. David Zhu, +0.838s8. Christopher Zanella, +0.987s9. Daniel McKenzie, +1.069s10. Kevin Mirocha, +1.123s