With all eyes on the Pogba brothers, playing against each other for the first time in competitive football, Ibrahimovic stole the show, taking his record against St Etienne to 17 goals in 14 appearances.
The result puts United in a strong position to advance to the last-16 of the Europa League ahead of the return leg in France next Wednesday.
Jose Mourinho named a strong team, making two changes from their victory over Watford as Paul Pogba lined up against older brother Florentin.
The St Etienne left-back was part of an unchanged XI for Christophe Galtier and the French side almost capitalised on a sloppy United start inside three minutes.
Eric Bailly’s blind backpass presented an opening to Romain Hamouma but with Sergio Romero out of position the forward failed to find a team-mate.
Instead, the hosts took the lead thanks to a huge slice of fortune when Ibrahimovic’s free-kick, awarded for a questionable foul on the Swede, clipped Vincent Pajot in the wall and wrong-footed Stephane Ruffier