Pavon recovered from a bogey at the first hole to pick up five birdies in the remainder of his round at the Torrey Pines South Course.
After his eight-foot birdie putt at the 18th, he roared in celebration and then hugged caddie Mark Sherwood.
Pavon, who won on the DP World Tour at the Spanish Open in October, said: “I can’t thank the PGA Tour enough to give us the opportunity to come from Europe and compete here in America against the best players in the world.
“That’s always been the dream for me. I got finally a shot and I took it.
“I think it is historic for French golf. We have Celine Boutier, the French LPGA player who won Evian last year, which is an even bigger performance.”
Hojgaard finished in second after a 70 while Germany’s Stephan Jaeger and American duo Nate Lashley and Jake Knapp tied for third place on 11 under.