Two goals in five minutes by Donovan Wilson and Joe Kizzi gave the Yellow Army their fourth win in the last five matches.
Northampton saw their winless run extended to three matches as they lost at home for the first time since August 21st. The Cobblers failed to register a single shot on target.
Story of the match
Northampton were dealt a blow right before kick-off as defender Jon Guthrie was ruled out after testing positive for COVID-19.
Sutton looked to take immediate advantage of the makeshift Cobblers' back-line as Liam Roberts had to be alert to Wilson's drive from an acute angle.
The Yellow Army's leading scorer saw his header go wide and five minutes later only excellent reactions by Roberts kept Richie Bennett off of the scoresheet.
In the 41st minute, the visitors took a deserved lead as a corner by Enzo Boldewijn was glanced in by Kizzi with his head.
Just 30 seconds into the second half, the lead was doubled as Bennett found space between the lines and ge slipped in Wilson, who rocketed past Roberts.
It was nearly three right after Wilson scored as Craig Eastmond played in David Ajiboye, but he went well wide with his shot.
The Northampton goalkeeper needed to be at his best to prevent his side from falling further behind, denying Alistair Smith and Wilson before sticking out a leg to stop Boldewijn.
Sutton head home having claimed not only a dominant victory, but a third clean sheet in their last four matches after another excellent performance.
Man of the match: Donovan Wilson
Picked up his fifth goal of the season and could have had a couple more if not for the excellence of Roberts. Was a constant threat for the Northampton defense.