Hayden's lap of one minute and 40.755 seconds was nearly a second faster than that of Karel Abraham on the Cardion AB privateer Ducati. Ben Spies was third fastest on the new factory Yamaha.
"Considering that the conditions weren't perfect, it's positive that we quickly come close to my best time from yesterday," said Hayden. "Now we hope the weather will let us work well tomorrow, because we'd like to improve some details before Qatar, especially with traction in the fast corners."
With the track damp and conditions windy and cold, not much activity took place until after midday when a serious downpour rendered the circuit totally wet for a while, offering up the opportunity for some to work on wet set ups at least.
Others elected to sit out much of the day, including Hayden's team-mate Valentino Rossi.
Honda's Dani Pedrosa was one rider to make the most of the conditions, and the Spaniard completed 25 laps in total on the new 213V.
"I decided to go out when it started raining properly because it's always good to get some information about the behaviour of the bike in wet conditions before the beginning of the season, and even more important with a new bike," he said.
"Obviously, the set up of the bike was pretty standard on chassis and electronics, but I had good feelings riding it, the bike worked well and it gives me confidence.
"If it's not raining tomorrow we will go back to the testing programme we had planned for today: basically to try some new ideas for the chassis and the electronics and if we have time I'd like to do a race simulation."
Like his world champion team-mate Casey Stoner, Pedrosa didn't record any flying 'dry' laps, the pair ending the day 12th and 19th in the times respectively.
Stoner decided against any serious running in the conditions.
Spies said that he was 'happy with his wet set up', while team-mate Jorge Lorenzo also completed more than 25 laps in the rain.
"Today we started late because of the weather so we only managed to do 25 or 30 laps in wet conditions. Now we know that the bike is working quite well and is competitive, we were in second place in the wet behind Dani and the next rider, Cal Crutchlow, was a second behind.
"We still need to work on our electronics as we haven't got the perfect solution for Qatar. For tomorrow we haven't got anything new but we need to decide whether to put away some parts."
1. Nicky Hayden Ducati 1m40.755s
2. Karel Abraham Cardion Ducati 1m41.661s + 0.906s
3. Ben Spies Yamaha 1m41.726s + 0.971s
4. Alvaro Bautista Gresini Honda 1m42.711s + 1.956s
5. Hector Barbera Pramac Ducati 1m43.288s + 2.533s
6. Ivan Silva Avintia FTR-Kawasaki 1m43.613s + 2.858s
7. Franco Battaini Ducati 1m44.264s + 3.509s
8. Michele Pirro Gresini FTR-Honda 1m44.761s + 4.006s
9. James Ellison Paul Bird Aprilia 1m44.969s + 4.214s
10. Danilo Petrucci Ioda Aprilia 1m45.336s + 4.581s
11. Colin Edwards Forward Suter-BMW 1m47.968s + 7.213s
12. Dani Pedrosa Honda 1m49.822s + 9.067s
13. Jorge Lorenzo Yamaha 1m50.088s + 9.333s
14. Cal Crutchlow Tech 3 Yamaha 1m51.127s + 10.372s
15. Andrea Dovizioso Tech 3 Yamaha 1m51.702s + 10.947s
16. Mattia Pasini Speed Master Aprilia 1m51.772s + 11.017s
17. Stefan Bradl LCR Honda 1m51.778s + 11.023s
18. Casey Stoner Honda 1m51.856s + 11.101s
19. Valentino Rossi Ducati 1m51.910s + 11.155s
20. Randy de Puniet Aspar Aprilia 1m52.397s + 11.642s
21. Aleix Espargaro Aspar Aprilia 1m57.718s + 16.963s