Hayden, riding at full fitness for the first time since the end of the 2011 season, made best use of the drying end-of-day track to pull 0.9sec clear of satellite Ducati rider Karel Abraham during day two of the Jerez MotoGP test.
Given the changeable conditions - and fact that the likes of Jorge Lorenzo, Dani Pedrosa, Valentino Rossi, Casey Stoner, Cal Crutchlow and Andrea Dovizioso did not try for a late dry lap - Hayden didn't make a big deal out of his timesheet topping ride.
But he did feel positive about lapping within 0.25sec of his best Friday time, despite the odd wet patch.
“It's a shame about the weather because I'd like to take advantage of as much time as possible to work on the bike, since I lost so much time in the past few months,” said Hayden, sixth fastest and 1.4sec behind Casey Stoner on day one.
“That's how it was today though, and it does no good to complain, especially since I had the chance to try the GP12 in the rain for the first time, improving my feeling little by little.
“We took a long break when the track started to dry out, and we put on the slicks at the end, even though there were still some wet patches out there. I was able to do a couple exits to try the two little changes that we'd planned yesterday.
“Considering that the conditions weren't perfect, it's positive that we quickly come close to my best time from yesterday. 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.”
Factory Ducati team-mate Rossi finished the day in 19th, having set his best time in the wet. A 'lost day' was exactly what The Doctor didn't need as he fights to find a front-end set-up for the new GP12 in time for the new racing season.
“I'm sorry to have lost practically the entire day of testing, even if we still did three exits with wet tyres and a wet setup, to confirm the feelings we had in similar conditions at the last test,” said Rossi.
“Otherwise, there's not much to say. We couldn't work well today, but the forecast for tomorrow is better, so we hope to be able to continue working on the setup that we identified at the end of the day yesterday.”
Sunday will be the final day of official 2012 pre-season testing.