Defender Gary Doherty headed the home side in front on 33 minutes from caretaker boss Gareth Ainsworth's cross, before Rene Howe levelled for the visitors shortly before the break.
Ryan Jarvis nearly gave the visitors a share of the spoils, but was denied by on-loan goalkeeper Jordan Archer's acrobatic save.
The home side had the better of the early exchanges, with Doherty and Matt McClure coming close. Billy Bodin should have put the visitors ahead on 21 minutes, but the Welshman tamely shot wide.
After Doherty put Wycombe ahead following poor defending from the Gulls' back line, United's leading scorer Howe benefited from Nathan Craig's good work to pull the scores level.
However, Scowen's header from substitute Dean Morgan's cross shortly after the hour mark was enough to end the Chairboys' baron run of six defeats from their last eight games.