The Red Devils, who had already qualified for the last 32 of Europe’s second tier club competition, were pegged back and beaten by the Kazakhstan side.
Jesse Lingard had given the visitors an early lead in the 10th minute when his deflected low shot found the back of the net.
However, goals from Dmitriy Shomko and Di’Shon Bernard put the hosts 2-1 up in the second half as they wrapped up the three points.
Ole Gunnar Solskjaer opted to field one of the youngest teams in Manchester United’s history, with the squad boasting an average age of 22 years and 26 days.
And England legend Lineker chose to focus on the youth of the Red Devils squad as he offered a short update on Twitter after the final whistle.
Lineker wrote on Twitter: “You can’t win anything with kids. #MUFC.”
Meanwhile, former Red Devils midfielder Owen Hargreaves also offered his response to the result after the game.
“That’s the difference between kids football and men’s football,” Hargreaves told BT Sport.
“They punished the mistakes from the young kids, they didn’t take the chance and then it goes the other way.
“That’s something Ole will say they’ve got to learn. If the chance is there, you’ve got to take it.”
The result still left Man United top of their group on 10 points, having already sealed their spot in the next round.
The Red Devils will now switch their attention immediately back to Premier League affairs and their preparations for their home clash against Aston Villa on Sunday afternoon at Old Trafford.
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