Haydon, who had feared he might not able to race after crashing in qualifying, upped the power when it mattered most. "I knew it would be down to a manoeuvre on the final corner but I left it later than ever before. It was a really tough race but it worked out in the end," he said.
"After the crash in qualifying I thought I would struggle to be on the pace but this is just great. I couldn't have hoped for a better start to the season, but there is still a long way to go and a lot more winning to be done," he added.
Haydon now has 81 points in the championship, five ahead of the Kawasaki rider Chris Walker, who finished in second position, marginally ahead of Bayliss, who had earlier won the third round for the Ducati team by one-third of a second from Haydon, with Walker third.
Neil Hodgson, who had gone into the meeting at the Hampshire circuit leading the series, had a day of mixed fortunes, sliding out in the first race but rebounding to finish fifth next time out, just ahead of defending triple champion Niall Mackenzie.
The Scot had pulled out of the first race of the day when his visor misted up.
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