Brady Vail had a pair of goals (3,4) and Kerby Rychel scored his team-leading eighth of the season, as the Spits claimed sole possession of first place in the West Division and the Western Conference.
Jack Campbell won his fifth game in six starts, making 37 saves.
Austin Levi gave the Whalers their only lead of the night at the mark of the first period.
Vail's second of the night squared things at 3-3 with a little more than two minutes to play in the middle 20.
In overtime, Plymouth 's Tom Wilson was hobbled after blocking a shot and losing his stick, but couldn't make it to the bench. That left Duininck uncovered at the right point. He took a feed from Adrian Robertson and blasted one past Scott Wedgewood, who took the loss in goal for Plymouth (25 saves).
The Spits are on the road this weekend, with stops in Erie on Saturday and Brampton on Sunday afternoon.
SCORING
FIRST PERIOD
SECOND PERIOD
THIRD PERIOD
No Scoring
OT
Duininck (2) (Robertson, Rychel)
SHOTS