Much-maligned centre-back Maguire headed in the only goal 18 minutes from time before Onana saved Jordan Larsson's penalty with the last kick of the game. The English giants had lost their opening two Champions League group games for the first time in the club's history, but are back in contention for the last 16 thanks to a much-needed win.
One of United's greatest ever players, Charlton died on Saturday at the age of 86. A moving tribute was paid to the 1966 World Cup winner before kick-off as United boss Erik ten Hag laid a wreath in the centre-circle before a minute's silence was observed. Ten Hag urged his players to be inspired by Charlton's legacy after a difficult start to the season. But the Dutchman would have been disheartened by another insipid first-half performance.
The Danish champions were inches away from going in front after just five minutes. Maguire was caught in possession by Mohamed Elyounoussi and the former Southampton forward's cross was turned onto the post by Diogo Goncalves. The emotional atmosphere around Old Trafford prior to kick-off quickly turned to groans of frustration at the home side laboured to create anything of note before the break.
Ten Hag responded by introducing Danish international Christian Eriksen against his countrymen. However, it was not until two more big chances for Copenhagen to take a shock lead that United awoke from their slumber.