The win for the hosts was the Turkish champions’ first victory in Europe’s premier club competition.
United fell behind after 12 minutes when Edin Visca’s long pass found Demba Ba in acres of space and the striker ran forward before finishing neatly past goalkeeper Dean Henderson.
Basaksehir doubled their lead five minutes before halftime after Deniz Turuc nicked the ball from Juan Mata and passed to Ba who set up Visca to score.
Anthony Martial’s header two minutes later gave United hope but despite enjoying plenty of possession in the second half, they were unable to break down the Turkish side’s disciplined defence.
Basaksehir scored their first Champions League goals and clinched their first points in the competition on a historic night for the club.
“We played well in the first two games too, but finally we secured a win. This is a big result for us, we are really proud,” Visca said.
United, who beat last season’s runners-up Paris St Germain and RB Leipzig in their first two games, top Group H with six points from three matches.
Basaksehir have three after their first victory in the competition. Leipzig host PSG later on Wednesday.
United, who have made a poor start to the English Premier League season with three losses in their first six games, played poorly in the first half.
Although they showed greater urgency after the interval, they only managed one more effort on target.
Manager Ole Gunnar Solskjaer sent on Paul Pogba and Edinson Cavani as substitutes and in stoppage time Alexandru Epureanu brilliantly cleared off the line to prevent an own goal.
The shocking defeat also meant that United’s 18-match unbeaten away run in all competitions ended. (Reuters/NAN)