Dougherty finished the tournament at 22-under-par 194, tying a Senior Tour record for a 54-hole event. Raymond Floyd won the 1993 Gulfstream Aerospace Invitational at 22-under.
The aggregate score of 194 was one shot shy of the tournament record established by Gibby Gilbert in 1992 at the par-70 Loch Lloyd Country Club.
However, at the par-72 Tiffany Greens Golf Club, Dougherty set a new tournament record in relation to par.
Defending champion Gil Morgan shot 69 to tie for second place at 14-under with Walter Morgan (64) and Hugh Baiocchi (69).
Dougherty opened the event by shooting a career-best 10-under-par 62. He followed that with back-to-back 66s over the weekend to collect the $225,000 first-place prize.
This is the 53-year-olds second career tour title. He won last years Coldwell Banker Burnet Classic.
Full-field scores from the TD Waterhouse Championship