After a goalless first half in Abuja where Carlos Tevez missed a twice taken penalty-kick, United took the lead through Chris Eagles just five minutes into the second half.
Fifteen minutes later Tevez made ammends for his spot-kick miss to give United a two-goal advantage.
Pompey scored what only turned out to be a consolation goal in the final minute of the match with Jermain Defoe finding the net for Harry Redknapp's side.
United: Kuszczak (Amos, 75); Neville, Vidic, Evans (Cathcart, 65), Silvestre; Gibson (Possebon, 74), Carrick (O'Shea, 65), Scholes, Eagles (Cleverley, 80); Tevez (Giggs, 65), Campbell.
United's next pre-season fixture will be against RCD Espanyol at Old Trafford on Saturday, 2nd August.