Andy Dorman gave St Mirren an early lead on Saturday and Motherwell struggled with their passing game on the bumpy surface.
But they pushed more men forward after the break and finally carved out a chance for Hughes to finish in the 65th minute.
David Clarkson's shot was saved after 30 seconds after Keith Lasley had slipped the ball into the left channel, but Mark Howard had no other saves to make until the goal.
Motherwell had the majority of the early play and Marc Fitzpatrick headed over from four yards after Stevie Hammell whipped in a free-kick, but they were caught out in the 12th minute by St Mirren's first foray forward.
Billy Mehmet slipped the ball into the path of Dorman's run and the midfielder fired past Paul Quinn on the line after initially being stopped by Hammell's sliding challenge.
Motherwell never looked like levelling before the break as their passing moves broke down on the bobbly and barren surface.
John Sutton had set up the clash with a double in Monday's 3-0 win over Inverurie but he had made way for the fit-again Hughes, who played on the left of a three-man attack lacking physical presence.
St Mirren had brought in Mehmet alongside Jim Hamilton after Craig Dargo was ruled out with injury and their far simpler tactics of sitting in and playing the ball long saw them lead comfortably after a dire first half.
Mark McGhee switched to a 4-4-2 formation for the second half after introducing on-loan Celtic striker Cillian Sheridan for his debut in place of Lasley.
The Lanarkshire side showed more urgency to get the ball forward but their crossing lacked accuracy and they were still guilty of over-elaborating at times.
Mehmet had a half-chance to put the game beyond the hosts when a long ball eventually fell at his feet 20 yards out but he sliced badly wide.
McGhee brought on winger Darren Smith for Fitzpatrick as Motherwell pushed more men forward and the pressure paid off in the 65th minute.
Howard blocked brilliantly from Sheridan following Clarkson's near-post cross and Hughes blasted the rebound high into the net from 12 yards.
The visitors came out of their shell but both sides cancelled each other out in the final quarter of the game. However, Saints almost snatched a win in injury time when Scott Cuthbert ran on to Steven Robb's free-kick, only for Graeme Smith to produce a great close-range save from the defender's volley.
The supporters who endured this game are unlikely to be thrilled by the prospect of the replay - scheduled for Tuesday, February 17 - but the fresh pitch at the new St Mirren Park should ensure the second match has far more quality.