Greenwood rescued the 2018 champions with a cool and composed finish 17 minutes from time.
The 17-year-old also became United’s youngest goalscorer in European competition.
“We always know that in and around the box he is one of the best finishers we have got,” said United manager on Mason Greenwood.
United, on the back of a 1-0 win over Leicester, made a host of changes with youngsters getting a chance to impress.
Ole Gunnar Solksjaer included Greenwood, Tuanzebe, Gomes and Chong in the playing XI.
“Today was a great opportunity for them,” added Solskjaer.
With United failing to qualify for the Champions League last season, Europe’s second-tier could be a great platform for the youngsters to shine.
Despite dominating right from the off, United failed to convert their chances.
Brazilian midfielder Fred saw an early effort bounce back off the bar as United started strongly.
In the opening exchanges, Rashford was denied by Nenad Eric, twice in quick successions.
The Kazakh champions were in for a famous draw at the ‘Theatre of Dream’ before Greenwood beat Eric under his legs.
In the other Group L fixture, Partizan and AZ Alkmaar shared spoils after a 2-2 draw in Serbia.
Further, Premier League side Wolverhampton lost 0-1 to Portuguese outfit Braga at the Molineux.
Ricardo Horta scored the only goal of the match 19 minutes from time.