The two clubs are still in dispute over the Toffees' approach for the Portuguese just over a year ago, which Watford blamed for their slump in results and ultimately led to his sacking shortly after and his appointment on Merseyside in the summer.
Visiting fans, bizarrely waving toy snakes, voiced their views on the morals of Silva as the sides met for the first time since his departure, but it did not affect Everton, who took an early lead as another former Hornet Richarlison scored his eighth of the season.
But the hosts failed to press home their advantage and a Seamus Coleman own goal equaliser was quickly followed by Abdoulaye Doucoure power header before Ben Foster saved Gylfi Sigurdsson's spot-kick.
However, Digne picked the perfect moment to score his first goal for the club with a curling free-kick 50 seconds before the final whistle.
It extended Watford's winless run to six matches and denied them an historic first win at Goodison Park in 13 attempts.
Everton had lost only once in the last 11 home games and the confidence that run had given them, coupled with Andre Gomes having now taken full control of pulling the strings in midfield and Richarlison restored to a central striker role, meant they began brightly.
It took 15 minutes for them to break down their visitors, but still required an element of luck and an assistant referee's oversight.
Gomes powered into the penalty area, dancing past a couple of tackles, but, as he chased the ball, Theo Walcott, coming back from an offside position, touched it on.
However, there was no offside flag from Simon Long and Gomes cut back the ball for Richarlison to fire home his fourth goal in seven league appearances at Goodison Park this season.
The Brazil international was denied a second from Sigurdsson's pass by Jose Holebas' lunging interception six yards out, while the 6ft 4in Yerry Mina was booked for handball as he tried to force home another Sigurdsson cross.
Watford had been dreadful up to that point, but, in their one move of quality, Roberto Pereyra, having produced an exquisite outside-of-the-foot pass to release Ken Sema, failed to connect with his header.
Troy Deeney's cushioned volley then dropped just wide as the Hornets pressed and the already-booked Mina's challenge on Isaac Success on the edge of the area had manager Javi Gracia marching on to the pitch at half-time to unsuccessfully confront Kevin Friend after the referee did not award a foul.
Pereya's free-kick into the side-netting and Deeney forcing a low save out of Jordan Pickford soon after the break showed Watford were far from spent.
Former Everton forward Gerard Deulofeu was introduced on the hour as Gracia sensed the tide had turned, with Goodison offering a warm welcome to a former favourite.
However, the Spaniard's through-ball soon released Kiko and, when Pereya's shot rebounded off a post, Coleman was caught by surprise and the ball went in off his thigh.
Less than three minutes later Watford were ahead when Pereya's cross was met by Doucoure, whose powerful downward header could not be kept out by Pickford.
The madness was not over as Christian Kabasele inexplicably charged into Mina to concede a penalty, only for Sigurdsson to drill his spot-kick straight down the middle and Ben Foster saved with his legs – the Iceland international's second failure in three attempts.
Silva rang the changes with Ademola Lookman, Dominic Calvert-Lewin and Cenk Tosun all sent on, but their game became more disjointed and Watford looked the more likely to score.
The Everton manager's desperation saw him deploy Mina as a centre-forward for the six minutes of added time, but it was another defender in the shape of Digne who came to his rescue.