Funk had a bogey-free tournament and has gone 60 holes without a bogey since the 13th hole last week in the final round of the SAS Championship.
Also the winner at The Woodlands in Texas in May, Funk opened with consecutive 66s to take a one-stroke lead into the final round.
Funk made his first birdie of the round on No. 12 after hitting his second shot out of a fairway divot, and added a second birdie on No. 14. The birdies allowed Funk to keep a share of the lead with Waldorf, who began the day at 8 under but climbed into contention with six birdies. Waldorf finished with a 66.
Mark Wiebe, the winner last year in a playoff, also birdied No. 18 to move into third at 10 under. He had a 70.
Chip Beck, Jay Don Blake, John Cook, first-round leader Dan Forsman and Peter Senior tied for fourth at 9 under. Blake and Cook shot 68, Forsman and Senior had 70s, and Beck shot 71.
In other tournaments *
At San Martin, Calif., Sweden's Jonas Blixt won the Frys.com Open for his first PGA Tour title, holing a 4-foot par putt on the final hole for a one-stroke victory.
Blixt became third PGA Tour rookie to win this season, closing with a 3-under 68 for a 16-under 268 total. He earned $900,000 in the Fall Series event.
Tim Petrovic and Jason Kokrak tied for second. Petrovic had a 64, and Kokrak shot a 68.
* At Kuala Lumpur, Malaysia, Inbee Park rallied to win the LPGA Malaysia for her second victory of the year, closing with a 4-under 67 to beat fellow South Korean player Na Yeon Choi by two strokes.
Park finished at 15-under 269 and earned $285,000 to push her tour-leading total to $1,954,608.
* At Vilamoura, Portugal, Shane Lowry, of Ireland, won the Portugal Masters after a final-round 5-under 66 to edge out England's Ross Fisher by one stroke with a 14-under 270 total.