Cook, who lost a playoff to Bruce Vaughan at the Senior British Open Championship in July, started the day one shot behind second-round leader Jeff Sluman. After bogeying the first hole, he birdied three of the next four holes and was tied for the lead midway through his round with Jay Haas and John Morse.
A 25-foot birdie putt at the 10th hole gave Cook the lead for good on the way to a 54-hole total of 16-under 197.
Cook, who hadnt won since the AT&T last year, collected a winners check of $247,500 and pushed his earnings past $1.8 million this year.
Fergus birdied the final hole for a 65 and a 13-under finish. Morse, who shot a 6-under 29 on the front nine and finished at 63, and Haas (66) tied for third at 12-under.
Haas has a 126-point lead over Fred Funk in the Charles Schwab Cup going into the Cup championship next week in Sonoma, Calif.
Sluman, the 1988 PGA champ, fell short of his third Champions Tour victory with an even-par 71. He tied for fifth at 11-under with Bruce Fleisher (69).
It was the second straight week a player defended his title on the Champions Tour. Bernhard Langer repeated at the Administaff Small Business Classic last week near Houston.
The last time consecutive tournaments were won by repeat winners was in 2006 when Dana Quigley won the Greater Kansas City Golf Classic and Allen Doyle won the U.S. Senior Open at Prairie Dunes.