The clutch birdie capped a round of 3-under 69 for Funk, who finished at 15-under 201 for his second triumph of the season and eighth of his Champions Tour career.
Waldorf -- making only his fourth tour start -- birdied four the first seven holes to charge into contention but finished with four consecutive pars. He carded a 6-under 66 to end one stroke back at minus-14.
Defending champ Mark Wiebe registered a 2-under 70, claiming sole possession of third place at 10-under 206.
Swim Week Miami Beach 2014 [PHOTOS]