The reigning Formula Renault Eurocup champion, who topped the first day at Aragon last week before the rest of that test was cancelled due to snow, knocked Red Bull protege Antonio Felix da Costa off the top of the times at the end of the day.
Da Costa had led the way for much of the test, setting the pace in the wet morning session before trading blows at the head of the field with Kevin Magnussen when the track dried.
The Portuguese driver continued to set the pace when most of the field took new tyres in the final hour, but he was pipped to top spot in the dying moments as Vandoorne went fastest for Fortec.
"I didn't expect to be first," said the Belgian. "Obviously I was looking to put down a time but as soon as I went out on new tyres there was a red flag.
"The car performs well in qualifying conditions, and tomorrow I'll be using a race set-up more often."
By the end of the day 14 drivers had beaten Jules Bianchi's qualifying record from 2012.
Behind the top two, Will Stevens and Marco Sorensen were next up, followed by Draco team-mates Nico Muller and Andre Negrao.
Magnussen slipped to seventh by the end, just ahead of 2012 FR3.5 race winner Nick Yelloly, driving for Zeta Corse.
The Briton has already signed to race for Carlin in GP3 this year, but he returned to FR3.5 at Zeta's request as it wanted an experienced driver to help with its test programme.
Morning times:Pos Driver Team Time Gap Laps
1. Antonio Felix da Costa Arden Caterham 1m57.555s 30
2. Kevin Magnussen DAMS 1m59.814s + 2.259s 31
3. Sam Bird ISR 2m00.954s + 3.399s 32
4. Daniil Move Comtec 2m01.383s + 3.828s 19
5. Marco Sorensen Lotus 2m01.920s + 4.365s 34
6. Lucas Foresti Comtec 2m02.154s + 4.599s 31
7. Will Stevens P1 2m02.199s + 4.644s 39
8. Carlos Huertas Carlin 2m02.529s + 4.974s 29
9. Jazeman Jaafar Carlin 2m02.700s + 5.145s 47
10. Pietro Fantin Arden Caterham 2m03.065s + 5.510s 42
11. Nico Muller Draco 2m03.105s + 5.550s 37
12. Andre Negrao Draco 2m03.195s + 5.640s 36
13. Nikolay Martsenko Pons 2m04.596s + 7.041s 43
14. Yann Cunha AV 2m04.790s + 7.235s 46
15. Oliver Webb Fortec 2m04.913s + 7.358s 31
16. Sergey Sirotkin ISR 2m04.976s + 7.421s 37
17. Mikhail Aleshin Tech 1 2m05.200s + 7.645s 30
18. Nigel Melker Tech 1 2m05.350s + 7.795s 36
19. Stoffel Vandoorne Fortec 2m06.154s + 8.599s 25
20. Matias Laine P1 2m06.337s + 8.782s 41
21. Mihai Marinescu Zeta 2m07.220s + 9.665s 24
22. Norman Nato DAMS 2m07.316s + 9.761s 38
23. Marlon Stockinger Lotus 2m07.817s + 10.262s 42
24. Zoel Amberg Pons 2m07.857s + 10.302s 15
25. Arthur Pic AV 2m08.316s + 10.761s 12
26. Nick Yelloly Zeta
Afternoon timesPos Driver Team Time Gap Laps
1. Stoffel Vandoorne Fortec 1m46.745s 25
2. Antonio Felix da Costa Arden Caterham 1m46.773s + 0.028s 34
3. Will Stevens P1 1m46.943s + 0.198s 28
4. Marco Sorensen Lotus 1m46.979s + 0.234s 18
5. Nico Muller Draco 1m47.185s + 0.440s 31
6. Andre Negrao Draco 1m47.240s + 0.495s 24
7. Kevin Magnussen DAMS 1m47.281s + 0.536s 27
8. Nick Yelloly Zeta 1m47.584s + 0.839s 30
9. Carlos Huertas Carlin 1m47.684s + 0.939s 26
10. Nikolay Martsenko Pons 1m47.705s + 0.960s 42
11. Lucas Foresti Comtec 1m47.738s + 0.993s 35
12. Sergey Sirotkin ISR 1m47.775s + 1.030s 28
13. Mikhail Aleshin Tech 1 1m47.989s + 1.244s 38
14. Oliver Webb Fortec 1m48.021s + 1.276s 26
15. Norman Nato DAMS 1m48.127s + 1.382s 30
16. Zoel Amberg Pons 1m48.178s + 1.433s 24
17. Daniil Move Comtec 1m48.202s + 1.457s 29
18. Marlon Stockinger Lotus 1m48.307s + 1.562s 21
19. Matias Laine P1 1m48.372s + 1.627s 21
20. Pietro Fantin Arden Caterham 1m48.439s + 1.694s 36
21. Jazeman Jaafar Carlin 1m48.440s + 1.695s 41
22. Yann Cunha AV 1m49.211s + 2.466s 40
23. Nigel Melker Tech 1 1m49.703s + 2.958s 16
24. Sam Bird ISR 1m49.778s + 3.033s 8
25. Mihai Marinescu Zeta 1m50.220s + 3.475s 29
26. Arthur Pic AV 1m59.888s + 13.143s 4
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