The 57-year-old Pernice closed with a 2-under 70 in breezy and rainy conditions, breaking a tie for the lead with Montgomerie with an 8-foot birdie putt on the par-4 14th and adding a 15-footer on the par-3 15th.
"I hit two beautiful irons,'' Pernice said. "I hit a beautiful 7-iron on 15 and it just worked out perfect. And then I couldn't have drawn it up any better, I just cut a 6-iron back against the wind beautifully on 15 and man, it turned out beautiful.''
Pernice bogeyed the par-3 17th and two-putted for par from 15 feet on the par-4 18th.
"I kind of got a little careless there at 17,'' Pernice said. "Made it a little interesting.''
The former UCLA player overcame a bogey-double bogey start Friday to win for the fifth time on the 50-and-over tour, ending a drought that stretched to the 2014 Charles Schwab Cup Championship. The two-time PGA Tour winner had a 13-under 203 total. He had a 69 on Friday, and shot 64 on Saturday for a share of the lead with Brandt Jobe.
"To be able to come back and shoot 13 to win was very special,'' Pernice said.
Montgomerie parred the final five holes for a 70. The 53-year-old Scot won a month ago in British Columbia for his fourth tour title.
"Especially the start it got very breezy,'' Montgomerie said. "First nine was very, very difficult. Just miserable.''
Pernice had a different take on the conditions.
"Whenever you get a little moisture in southern California, you'd better take it,'' he said.
Scott Dunlap was third at 10 under after a 67. The top 72 on the money list earned spots at Sherwood, and the top 54 advanced to the Dominion Charity Classic next week in Richmond, Virginia.
The field will be cut to 36 for the season-ending Charles Schwab Cup Championship in Scottsdale, Arizona. Each dollar earned in the first two events is worth two points. At the Charles Schwab Championship, points will be reset so that the top five only have to win to capture the Charles Schwab Cup.
Pernice earned $305,000 -- and 610 points -- to jump from 32nd to ninth in the standings.
"It's been a little bit of an up and down year, but I just kept telling myself, 'Keep working hard and keep plugging away.'''
Pernice said "It's not always how you start but if you finish well you can have a great year.''
Charles Schwab Cup leader Bernhard Langer withdrew before the start Friday because of a left knee injury. The 59-year-old German star also leads with four victories and has wrapped up the season money title with $2,697,459. Montgomerie moved into second place in the standings. Jobe tied for 10th at 6 under after a 77.
Fred Couples had a 77 to tie for 37th at 1 over in his first tournament in eight months. The 57-year-old Couples was sidelined by a chronic back injury. He opened with rounds of 68 and 72.