The Red Devils looked to be making it successive wins over Man City when they took the lead in the 82nd minute of the contest through Alejandro Garnacho.
However, Bernardo Silva levelled the scores in the 89th minute, before the reigning Premier League champions triumphed in the penalty shootout.
Man United were missing Rasmus Hojlund, Tyrell Malacia, Leny Yoro, Victor Lindelof, Luke Shaw and Aaron Wan-Bissaka for the contest, and Facundo Pellistri finished the match at right-back.
Maguire, 31, was one of four players substituted just before the hour mark against Man City, and the centre-back had previously gone down in pain with an apparent issue in the first half of the contest.
Ten Hag reveals Maguire issue
According to the Man United head coach, Maguire suffered "a little knock" on Saturday, and he will now need to be assessed after the clash with Pep Guardiola's side.
"I just checked with the doctor, and the doctor was the person I spoke to most last season, and it seems that everyone is [starting to] come good," Ten Hag told reporters after the Community Shield.
"[There is] a little knock with Harry [Maguire] but we hope he can keep fit and available for next week when we start the season against Fulham."
Lisandro Martinez started at left-back against Man City, with Jonny Evans joining Maguire in the middle, but Matthijs de Ligt could be an option for next Friday's Premier League opener with Fulham, as the Netherlands international is said to be on the verge of arriving at Old Trafford from Bayern Munich.
Which players will definitely miss out against Fulham?
As it stands, Man United have three definite absences for the game against Fulham, with Yoro, Hojlund and Malacia unavailable for selection.
Yoro will be missing until November due to a fractured foot, while Hojlund is out until September with a hamstring issue, with both players picking up their problems against Arsenal during pre-season.
Malacia has not played since the 2022-23 campaign due to a serious knee injury, meanwhile, and he will not be back in the fold until the latter stages of this year.
Wan-Bissaka is set to join West Ham United, but Shaw is expected to be available for the clash with Fulham.
Lindelof could also be back, although the Sweden international is believed to be surplus to requirements, with De Ligt's arrival potentially signalling the end of his time at Old Trafford.