Town suffered late heartbreak at Gander Green Lane as Craig Eastmond's 80th minute volley sent Sutton into the last four of the Papa John's Trophy.
Town had gone toe to toe with their third place opponents, but were undone ten minutes from time as a corner dropped to the U's Skipper, with Luke Armstrong going agonizingly close to a dramatic equalier, but striking the base of the post three minutes from time.
Simon Weaver returned to the dugout having missed Saturday's win with a positive Covid test and recalled Nathan Sheron to the starting line-up, the versatile defender replacing the cup-tied Lewis Richards.
In the Sutton camp, five changes were made, with Captain Eastmond making his 300th club appearance, following Warren Burrell who achieved the same feat at Town on Saturday against Oldham.
The first chance went the way of the hosts as Enzio Boldewijn wrestled the ball away from Brahima Diarra before firing into the side netting.
Pressure in the final third then lead to Town's first chance as Jack Muldoon won possession and pulled the ball back from the byline, but Sutton were able to block the attempts of Luke Armstrong and Lloyd Kerry.
Town's top scorer Armstrong was the first player to force a save from either 'keeper as his 27th minute strike was well read by Dean Bouzanis who comfortably claimed.
Town finished the half the stronger with Lewis Page almost forcing an own goal with a low cross after an incisive Josh Falkingham pass, though the sides went into the break all square.
The hosts' first effort on target came four minutes into the second half as Eastmond tried his luck from the edge of the box, with Mark Oxley beating away the effort.
Diarra then went close to breaking thre deadlock as he beat two Sutton player before seeing his shot deflect kindly into the path of Bouzanis.
Home Manager Matt Gray opted for a triple change on the hour mark, introducing Omar Bugiel, Isaac Oloafe and Alistair Smith, while Town were forced into a change minutes earlier with Will Smith replacing the injured Page.
Muldoon went close to opening the scoring in some style with just over 15 minutes to go as he expertly brougt down an aerial ball and poked towards goal, only for Bouzanis to again go the right way and save.
The decisive moment arrived in the 80th minute when after some head tennis in the Town area from a Sutton corner, Captain Eastmond struck a volley hard and low past Oxley to put his side ahead.
Town tried all they could to level late on and send the tie to a penalty shoot out, with Armstrong striking the base of the post in the 87th minute the closest Weaver's side would come to an elusive equaliser.
Town: Oxley, Page (Smith 53), Falkingham, Burrell, Thomson, Sheron, Kerry (Beck 82), Muldoon, Diarra (Pattison 66), McArdle, Armstrong
Subs not used: Cracknell, Austerfield
Booked: Armstrong, Page, McArdle
Sutton: Bouzanis, Wyatt, Goodliffe, John, Davis (Smith 60), Randall (Ajiboye 65), Eastmond, Boldewijn, Kizzi, Wilson (Oloafe 60), Bennett (Bugiel 60)
Subs not used: Nelson, Korboa, Milsom
Goals: Eastmond 80
Booked: Davis, Smith
Referee: S Allison
Attendance: 1,499 (71 away)
Davis (Smith 60)
Randall (Ajiboye 65)
Wilson (Oloafe 60)
Bennett (Bugiel 60)
Page (Smith 53)
Kerry (Beck 82)
Diarra (Pattison 66)