Going into the match United needed three points to ensure Premier Division safety, but Basingstoke got off to a good start when Emsden headed over Andy Lomas after just 7 minutes to put the visitors ahead.
Unfortunately United failed to perform until the last fifteen minutes, aided by the introduction of subs Kevin Davies and Mick Swaysland.
Greg Howell (29) and Aiden O'Brien (31) both hit a post before slack marking allowed Coombs to put Stoke 2-0 up (43).
On 70 mins Wilkinson was about to be cautioned for a foul and was sent off for dissent, and United pulled a goal back on 73 minutes when Swaysland crossed for Davies to head home.
In a 'cup-tie finale' Davies almost salvaged a point but hit the underside of the bar.