Mallinger, who lost his fully exempt PGA Tour status after finishing 133rd on the money list, made a 25-foot birdie putt on No. 18 to finish at 15-under 273 in the event featuring 76 male and female players. He earned $60,000 in the $300,000 tournament sponsored by Callaway Golf.
Mallinger, who also led after the second and third rounds, had eight birdies, two bogeys and a double bogey in the final round played in intermittent rain.
"I putted well today and putted well all week," said Mallinger, who has eight top-three finishes but is winless since joining the PGA Tour in 2006. "I love Pebble Beach. It's tough to beat Pebble Beach."
Gore, who will join Mallinger in the PGA Tour's final qualifying tournament, closed with a bogey-free 65.
"I tried, but I just got outplayed," said Gore, who also birdied the final round. "But I played well and I'll take the momentum to Q-School."
Pat Perez (65) and Champions Tour player Russ Cochran (71) tied for third at 11 under. Cochran, who began the final round trailing by one stroke, held a one-stroke lead after birdieing the 11th but bogeyed the 13th and Mallinger soon began his final birdie spree.
Annika Sorenstam, completing her first 72-hole tournament since her LPGA Tour retirement in 2008, shot a 73 to finish at 3 under.
"It's funny, you don't play for two years and then you go inside the ropes and the mindset comes back," Sorenstam said. "It's there, which is too cool. But you can't make the same shots anymore."
Morgan Pressel shot a 72 to finish at 7 under, the best among the 13 LPGA Tour entrants.
Tommy Armour III, the 2008 and 2009 winner, withdrew before the final round because of personal reasons.