Pruett and Rojas were among the teams caught out by the changing conditions, finishing tenth in the #01 TELMEX Lexus Riley. They entered the race three points ahead of Gurney and Fogarty, while Angelelli and Brian Frisselle were 14 points back.
Despite the on-and-off rain, there was only one brief full-course caution, when Ozz Negri spun on lap 41 after contact with Rob Finlay. The race's average speed fell to 89.526 mph (144.078 kph).
The biggest incident occurred before the green flag, when NASCAR Sprint Cup Series regular Carl Edwards spun into a guardrail in Turn 11. He and fellow NASCAR star Marcos Ambrose planned to make their Daytona Prototype debut in the Doran Racing #77 Aflac/iRacing/Au Vineyards Ford Dallara.
"The tyres with these cars take so long to get grip and are so much different than what I'm used to," said Edwards, who qualified seventh. "I worked the tyres in as good as I could, and I just got a little too aggressive at a medium speed corner and it swapped. I feel terrible."
Meanwhile Robin Liddell passed Andy Lally for the GT lead and then led the final 18 circuits to give the #57 BryanMark Financial/Stevenson Automotive Pontiac GXP.R its second consecutive Montreal 200 Acxiom GT victory and third triumph of the 2009 campaign.
"This was one of the hardest races I've ever run, especially when we were out there in the rain on slick tyres," Liddell said. "It seemed we were on a knife's edge, everywhere. At one point, I spun and lost a few positions. Then I had a great battle with Andy Lally. I got by, and all of a sudden we were in the lead. It was a great result. We're over the moon about that."
Lally and NASCAR Nationwide Series regular Brendan Gaughan took second in the #66 AXA/South Point Casino Porsche GT3.
"It's all about the team and the guy I drove with," Gaughan said of his Rolex Series debut. "It was unbelievable doing the wet-to-dry thing. But Andy Lally and (car owner) Kevin Buckler kept talking to me and keeping me cool. I did what I wanted to do, and then handed it over to Andy."
Taking third were Crown Royal 200 at The Glen co-winners Emil Assentato and Jeff Segal in the #69 FXDD SpeedSource Mazda RX-8.
The competitive GT race had eight different drivers and seven cars taking turns in the lead. Leh Keen led 17 laps from the pole in the #87 Farnbacher Loles Racing Porsche GT3, with Dirk Werner getting caught out in the changing conditions to finish sixth. Despite their worst 2009 result since taking eighth in the Rolex 24, the four-time winners padded their lead to 35 points over Kelly Collins, who took tenth in the #07 Drinkin' Mate Pontiac GXP.R shared by Paul Edwards. The victory allowed Davis to move into third, 43 points behind the leaders.
Tom Sutherland led a race-high 20 laps in the #30 Click-Away Computers/3Dimensional.com Mazda RX-8, but finished eighth after co-driver Dane Cameron was forced to stop to avoid hitting the spinning car of Charles Espenlaub late in the race. Espenlaub led a lap and finished fourth in the #40 Dempsey Racing Mazda RX-8 started by Joe Foster, matching the team's best result of the season.