The Swede scored the first on 15 minutes after his free-kick was deflected off the wall but still trickled over the line.
His second was even more effortless as in the 75th minute Rashford beat two defenders to the byline and then cut it back to Zlatan, who only had to tap it in from a couple of meters out.
Saint Etienne missed one of their best chances in the game to pull one back and on 87 minutes, just when it looked United would be content with a 2-0 win, Ibrahimovic was brought down in the area under a challenge from Theophile-Catherine and the referee showed the penalty spot.
Zlatan took the penalty himself of course to seal the final score and give United a fantastic cushion ahead of the second leg in France.