After Asier Hierro’s converted an 11th-minute free-kick for the visitors, the young Reds had to work hard to find openings against an organised Athletic side.
Substitute Gabriele Biancheri provided the inspiration, with a driving run down the right-wing and a cut-back to James Scanlon, who provided a smart, first-time finish.
Biancheri then netted an injury-time winner from Jack Fletcher's cross.
Travis Binnion’s United side will face Anderlecht (Leigh Sports Village) and Borussia Dortmund (Old Trafford) in December, before welcoming Sporting in January.
FIRST HALF
United’s intentions were clear from the whistle: play with pace and intensity.