After a goalless first half, with Everton's Tom Davies, Ross Barkley and Phil Jagielka all testing the Watford goalkeeper, Heurelho Gomes, the deadlock was broken on 56 minutes when Barkley scored from 25 yards.
Everton chased a second, with Kevin Mirallas, Romelu Lukaku and Enner Valencia all having attempts on goal.
Watford's best chance came from an Etienne Capoue corner headed narrowly wide by Adrian Mariappa.
The win means Everton won 43 points at Goodison in 2016/17, their best total in the Premier League.
They remain seventh with 61 points while Watford, after a fourth straight league defeat, are 15th with 40 points.