With a 5-0 demolition of Hibernian in their play-off round first leg on Wednesday, Aston Villa all but guaranteed a Conference League group-stage place.
The Premier League club kicked off their first European season since losing in Europa League qualifying in 2010.
Watkins headed home Lucas Digne’s cross in the 17th minute for Unai Emery’s men, who defeated Everton 4-1 the previous weekend.
Hibs had a penalty claim turned down soon after, but any thoughts of an upset were dashed when Watkins and Leon Bailey placed former European champions Villa three goals ahead before halftime.
Watkins finished another Digne cross less than three minutes into the second session to complete his triple.
Douglas Luiz scored from the penalty spot with 16 minutes remaining, allowing Emery to rest players for the second leg next week.
In the other match on Wednesday, Dnipro-1 drew 1-1 with Trnava in Slovakia.