Ellington (6) had the Hornets in front when he fired in from inside the box, but Leon Best headed Coventry level just before the hour mark.
Coventry had looked likely to grab a winner, but a defensive mistake from former Watford man Stephen Hughes allowed Smith to score 11 minutes from time.
Watford took the lead when Ellington picked the ball up 30 yards out before driving the ball past Kasper Schmeichel.
Sub Michael Mifsud tehn laid the ball off to Julian Gray on the left and he dinked in a cross right into the path of Best who headed home.
However, Richard Lee’s long kick was misjudged by Hughes who allowed the ball to bounce over his head and into the path of Smith who slipped the ball home.