Mbemba scored both his goals in the second half of the final played behind closed doors in Coimbra.
Victory allowed Porto to complete a league-cup double but they did it the hard way.
Their Colombian winger Luis Dias was sent-off in the 38th minute with coach Sergio Conceicao also receiving a red card five minutes later.
Mbemba headed in the opener from a free-kick two minutes into the second period and repeated the trick from another set piece on the hour mark.
Benfica cut the deficit in the 84th minute from the penalty spot with Carlos Vinicius tucking the ball away.
Benfica's Jota then saw a shot come back off the post in the last minute.