Funk and DiMarco combined for a nine-under 62 to win the two-day event at 19- under-par 123.
Dana Quigley, the Champions Tour's leading money winner, and his nephew Brett tied for second place with Sergio Garcia and Brad Faxon. The second-place finishers tied at 17-under-par 125.
DiMarco, who lost in playoffs at the Masters and PGA Championship, sank a 22- foot birdie putt on the 18th to give the U.S. Ryder Cuppers their two-shot win.
Davis Love III and Lucas Glover teamed for a 62 to take fourth place at minus-16. Scott McCarron and Tim Herron shot a final-round 63 for fifth at minus-15 and Bill and Jay Haas paired for a 64 to take sixth at 14-under-par 128.
The CVS Charity Classic features 10 two-member teams competing in a 36-hole, best-ball format with a total purse of $1.2 million. The event was first played in 1999 and has since raised close to $5 million for charity.