The Frenchman came out on top in a session blighted by red-flag stoppages, while his DAMS team-mate and championship leader Kevin Magnussen will start from the back after he suffered a fuel pressure problem.
Nato set his best time in the longest run of activity without a stoppage, initially edging Stoffel Vandoorne for pole before Magnussen's stoppage brought out the red flag.
But in the final burst of green flag activity there were more improvements behind the pole man, with Carlos Huertas, Sergey Sirotkin and Arthur Pic all getting ahead of Vandoorne.
By causing a red flag, Magnussen had his best lap deleted, but that made little difference to his fortunes as he was yet to set a representative time before going off.
The Dane's misfortune gives his closest challengers in the title fight a chance to make up some ground following his victory in race one.
While Pic and Vandoorne are in the top five, Red Bull junior Antonio Felix da Costa will start ninth.
Qualifying had been shortened from 30 to 15 minutes due to an oil consumption problem discovered after the first race, but the organisers had to add another five minutes to the session as at one stage there were only seven minutes to go and nobody had been able to set a time due to the red flags.
Pos Driver Team Time Gap Laps
1. Norman Nato DAMS 2m12.303s 10
2. Carlos Huertas Carlin 2m12.512s + 0.209s 9
3. Sergey Sirotkin ISR 2m12.611s + 0.308s 8
4. Arthur Pic AV Formula 2m12.896s + 0.593s 10
5. Stoffel Vandoorne Fortec 2m13.026s + 0.723s 10
6. Will Stevens P1 2m13.156s + 0.853s 8
7. Nico Muller Draco 2m13.195s + 0.892s 9
8. Andre Negrao Draco 2m13.235s + 0.932s 9
9. Antonio F. da Costa Arden Caterham 2m13.683s + 1.380s 9
10. Matias Laine P1 2m14.315s + 2.012s 7
11. Mikhail Aleshin Tech 1 2m14.677s + 2.374s 8
12. Christopher Zanella ISR 2m15.195s + 2.892s 8
13. Marco Sorensen Lotus 2m15.244s + 2.941s 8
14. Nigel Melker Tech 1 2m16.053s + 3.750s 7
15. Pietro Fantin Arden Caterham 2m16.617s + 4.314s 9
16. Daniil Move Comtec 2m16.961s + 4.658s 8
17. Matheo Tuscher Zeta Corse 2m17.226s + 4.923s 8
18. Yann Cunha AV Formula 2m17.877s + 5.574s 9
19. Oliver Webb Fortec 2m18.056s + 5.753s 9
20. Mihai Marinescu Zeta Corse 2m18.715s + 6.412s 8
21. N.Martsenko Pons 2m19.761s 7.458s 7
22. M.Stockinger Lotus no time 7
23. Jazeman Jaafar Carlin no time 7
24. Lucas Foresti Comtec no time 7
25. Kevin Magnussen DAMS no time 7
26. Zoel Amberg Pons no time 7
The 2015 Formula Renault 3.5 season will be notable for being the last with the French company's backing but also produced a worthy champion in Oliver Rowland. PETER MILLS evaluates this year's crop of drivers
Last year's field was extraordinary and hard to match, but the Formula Renault 3.5 grid will still have plenty of talent this season. Glenn Freeman runs through the field ahead of this weekend's season opener
Landing the Fortec seat that took rising star Robin Frijns to the 2012 FR3.5 title was already a good sign for Stoffel Vandoorne. Then McLaren took him under its wing. Peter Mills tells Vandoorne's story so far