Saint-Etienne were the Swede’s favoured prey during his time with Paris Saint-Germain and his treble took his tally against the French side to 17 goals in 14 games, and 23 for the season.
Victory gives Jose Mourinho’s side one foot in the last 16 ahead of Wednesday’s return leg, although things would have been very different had Nolan Roux not spurned a chance just before United’s second goal.
As it is, United are unlikely to miss Ander Herrera at the Stade Geoffroy-Guichard after he received a booking for handball that will incur a one-game suspension.
The win meant United star Paul Pogba came out on top in his first competitive appearance against his elder brother, Florentin, and he came close to scoring with a header that hit the bar.
Prior to kick-off, Saint-Etienne’s fans lit up Old Trafford’s East Stand with a mass of red and green flares.
Smoke hung above the pitch at kick-off and there was a distinct fogginess to Eric Bailly’s first contribution, with his careless back-pass almost letting in Romain Hamouma.
But after Anthony Martial had warmed Stephane Ruffier’s palms from 25 yards, United went ahead in the 15th minute in doubly soft fashion.
Ibrahimovic was awarded a free-kick despite minimal apparent contact from Jordan Veretout and the Swede’s shot struck Vincent Pajot in the wall before rolling tamely past the grounded Ruffier.
United had two good chances to extend their lead, with Juan Mata seeing a volley saved by Ruffier from Pogba’s clever lofted pass.
Martial then tore through the visiting defence before dispatching a low shot that Ruffier blocked with his left foot.
– Perrin dazed –
Ibrahimovic instinctively scuffed the rebound goal-wards, but over the bar.
Saint-Etienne began to exploit pockets of space in United’s half as the first period wore on, however, and Hamouma in particular gave them some uncomfortable moments.
Mourinho sent on Jesse Lingard for Marouane Fellaini at the break in a bid to keep the play in Saint-Etienne’s half.
But while the early skirmishes all took place in and around the visitors’ box, they had more to do with flailing limbs than dashing football.
Martial was booked after catching Kevin Malcuit with his left forearm, which left the Saint-Etienne right-back spitting blood.
A clash of heads between Chris Smalling and Loic Perrin, the two captains, left both on the turf, but although Perrin in particular seemed dazed, both men stayed on.
Saint-Etienne were beginning to live dangerously, with Ruffier blocking from Martial and Antonio Valencia and Pogba shooting inches wide.
Pogba’s influence continued to grow and he came within inches of doubling United’s lead by slamming a header against the bar from Daley Blind’s free-kick.
Four minutes later Saint-Etienne squandered a huge chance to level as Ole Selnaes picked out fellow substitute Roux, only for the former Lille man to loft his shot onto the roof of the net.
It was a miss they quickly came to rue as United substitute Marcus Rashford darted to the byline on the left and centred for Ibrahimovic to tap in his second in the 75th minute.
The United No 9 had the last say with two minutes left, steering a low penalty past Ruffier after he had been caught on the heel by Kevin Theophile-Catherine.