The hacking challenge kicked off at the CanSecWest security conference, which runs from March 9 to 11 in Vancouver, British Columbia.
A team from the French security company Vupen walked off with $15,000 and a new MacBook Air after exploiting an unpatched vulnerability in Safari.
Apple had updated Safari to version 5.0.4, fixing 62 vulnerabilities. But Vupen was still able to break the browser.
"Apple has just released Safari 5.0.4 and iOS 4.3 a few minutes before the Pwn2Own contest," Vupen said on its Twitter account several hours before the contest began. "This breaks some exploits but not all!!"
HP TippingPoint, the security company that sponsors Pwn2Own, said earlier today that the last-minute Safari updates could affect who was awarded prize money.
TippingPoint's Peter Vreugdenhil said the browsers were "frozen" two weeks before today's tip-off with the then-current versions of Safari, Google's Chrome 9, Microsoft 's IE8 and Mozilla's Firefox 3.6, to give researchers a stationary target.
"Exploit development does sometimes rely on certain versions and that is the reason we have frozen the devices," Vreugdenhil said.
But the Safari patches still had a part to play in Vupen winning. If the vulnerability used by Vupen to hack Safari had been fixed in 5.0.4, TippingPoint would not have been awarded the $15,000 prize.
Instead, the money would have gone to the first researcher who exploited the 'frozen' version of Safari - 5.0.3 was on the MacBook Air - using a bug still present in today's update.
See also: Apple 'to patch Safari before Pwn2Own'