Svilar, who became the youngest goalkeeper to start a Champions League game aged just 18 years and 52 days, caught the ball but in doing so stepped backwards over his line to gift United the lead.
It will be played at the Estadio da Luz in Lisbon.
Reuters/Lucy NicholsonDavid de Gea training with Manchester United, July 14, 2017.
But the youngster - who beat Iker Casillas' record to become the youngest keeper in the Champions League at 18 years, 52 days - took up an terrible position.
And Mourinho informed his players to take advantage of Benfica's inexperienced goalkeeper Mile Svilar, 18.
The hosts nearly took advantage of United's setup in the 14th minute, but Eduardo Salvio smashed a left-footed effort considerably wide from 12 yards after Alex Grimaldo had brilliantly dribbled past three challenges, linked with Pizzi and crossed into the centre.
Romelu Lukaku responded with a header that smashed back off the crossbar, but referee Felix Zwayer whistled for an infringement as the match returned to its plodding pace.
United finally tested the inexperienced Svilar for the first time nine minutes before the interval - Nemanja Matic drilling an effort at him from a narrow angle after driving into the left side of the area.
Rashford would soon limp off to be replaced by Anthony Martial, with the in-form substitute swiftly showing great skill before having a near-post attempt stopped as the match petered out.
United successfully held on to what proved to be a straightforward win, with Luisao's red card for second bookable offence after a rash tackle on Scott McTominay compounding a bad day for the home side.