Rea took himself out of the podium equation on lap four when he made a failed attempt to punish a small mistake by Xaus, the Ten Kate Honda rider having to sit up and allow the two Yamahas through instead.
Two became one Yamaha on lap five though when it was revealed Haga would have to observe a drive-thru penalty for jumping the start. Cementing his loss of second place in the standings, Haga's indiscretion left the battle for second place between Xaus, Checa and Michel Fabrizio.
Corser had been part of the fight but almost as soon as Haga pitted, he dropped back with an error at turn one on lap six to slip down the order again.
Having crashed out on the first lap in the earlier race, Fabrizio was determined to make amends and go into the off-season on a high, although he didn't help himself initially with one of his trademark slow starts.
Nonetheless, he was on a charge up the order, passing Rea for third on lap six before embarking on an enjoyable tussle with Xaus for second, the Italian eventually getting the better of his Ducati counterpart on lap nine.
Rea, meanwhile, was about to drop of the reckoning altogether when he was caught out in a three-way scrap heading into turn one. Caught out on the outside, Rea couldn't lean in and was simply forced to bobble over the gravel trap and out of the points.
Rea's demise wasn't the only surprise on lap ten though as Xaus' valiant attempts to stay second eventually ended with him high-siding at the final corner. Although he almost caught the wayward Ducati as it snaked beneath him, it eventually gave way at considerable speed, throwing Xaus to the ground, albeit thankfully unharmed.
His accident was bad news for Checa though, who had been stalking him closely at that point, the Honda rider forced to take a long route around the rider-less bike to drop from third to tenth.
With the order shaken up, Bayliss now had a clear lead over Fabrizio at the half way point, while Max Neukirchner was now up to third, the German having picked off his rivals carefully from a lowly 15th on the grid as he looked at the prospect of being rewarded with a possible podium at the end of what has been a breakthrough season.
Corser was back up to fourth, ahead of Crutchlow and Haslam, although the latter rider would pass his team-mate soon afterwards to snatch fifth. Like Neukirchner, Fonsi Nieto
was putting in a good show for Suzuki in seventh, while Regis Laconi
was producing Kawasaki's most convincing performance for some time in eighth.