The Spaniard crossed the line in 6 hours, 57 minutes, 28 seconds ahead of Boonen and Italy's Alessandro Petacchi after breaking from a pack of 25 riders.
The Rabobank rider also won the opening single-day classic of the season in 2004 and 2007.
“The start was tough, but I think it went well for me and I didn't panic,” Freire Gomez said. “My training has been very hard, but it meant I could stay strong at the end.” The riders remained bunched coming down the final ascent of the 298-kilometer (185-mile) race. Frenchman Yoann Offredo was the first to make a break after the descent, but he was caught by the pack.
Filippo Pozzatto made another unsuccessful break with two kilometers (1.2 miles) remaining, while Freire Gomez bided his time in the pack before launching his attack over the last few meters.
“This year is going very well, but now I have to keep winning,” Freire Gomez said. “The team prepared me well and the praise should go to them.
Lance Armstrong pulled out the race Friday, citing acute gastroenteritis.
