Waddle scored on a 3-yard catch and run with 10:51 remaining in the third quarter, giving the Dolphins a 17-10 lead over Jones and the Patriots.
Waddle now has four catches for 61 yards.
DeVante Parker set up the score in the nine-play, 75-yard drive, catching a 30-yard pass from Tagovailoa along the sideline on third-and-eight. Parker has two catches for 53 yards.
Tagovailoa now has completed 12 of 21 passes for 173 yards and a score.