The former Paris Saint-Germain striker came off the bench midway through the first half to replace the injured Paul Pogba on Thursday night but was quickly involved in an altercation with Danish defender Kjaer.
Ibrahimovic appeared to trip Kjaer as the ball went out of play but when the Dane tried to prevent him from taking a quick throw in, the 35-year-old grabbed him by the throat and shouted in his ear.
There was no action taken at the time as while the fourth official separated the pair, referee Milorad Mazic appeared to miss the incident.
However, the clash was clearly seen on television footage and Uefa officials could take some form of action against Ibrahimovic.
The former Sweden captain has been struggling for form of late and has only scored once in his last 11 games for United in all competitions.
United fell behind from a stunning overhead kick from Moussa Sow in the second minute before Jeremain Lens curled in an equally brilliant free kick in the second half.
Wayne Rooney pulled a goal back late on with a 25-yard piledriver, but it was not enough as the Red Devils lost their second Europa League game of the season.
Jose Mourinho’s side now sit in third place in Group A, one point behind both Fenerbahce and Feyenoord with only two games left to play.
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