Couples, who led by two shots after 36 holes, finished the day comfortably on top at 15-under-par 198 at TPC Harding Park as he seeks his first Champions Tour win of the season.
Mark O'Meara (67) grabbed sole possession of second place at 10-under 203.
Sixth place at minus-8 was held by Mike Goodes (69).
This is the last event on the Champions Tour this year. The Charles Schwab Cup and the $1 million that goes with it will be awarded at the end of the tournament and the only players with a chance to win the year-long points race are Kenny Perry and Bernhard Langer.
The only way Langer can overtake Perry would be to win this tournament while Perry finishes outside the Top 5.
Langer shot even-par 71 to drop into a tie for seventh place alongside Perry (67) and Rocco Mediate (66) at 7-under-par 206.