The 23-year-old sat out the trip to Craven Cottage with a shin problem sustained in last week's League Cup defeat to Brighton.
He will miss two matches against Scotland and games against North Macedonia and Switzerland.
"Manchester United can confirm that Benjamin Sesko has withdrawn from the Slovenia squad ahead of the upcoming three-week international break," the club said in a statement on Monday.
"Benjamin will undergo tests this week before defining his individual recovery plan."
Sesko, who has scored two goals for United this season, became the fourth player from the club to pull out of international duty on Monday.
Marcus Rashford and Kobbie Mainoo are both out of England's squad, while Karl Darlow withdrew from the Wales camp.
Michael Carrick's United are a lowly 12th in the Premier League table after taking just five points from their opening five games.
Their next match is at home to bottom side Tottenham on October 10th.
English Premier League
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