The Red Devils, who will contest Group G with England, Panama and Tunisia at the World Cup, had to come from a goal down after former Fulham man Bryan Ruiz opened the scoring with a strike from distance with 24 minutes gone.
However, strikes from Dries Mertens and Michy Batshuayi either side of a Romelu Lukaku brace ensured Roberto Martinez men travel to Russia on the back of a confidence-boosting win.