Former loanee Hallam Hope came back to haunt the Cobblers with the opening goal as Bury inflicted a costly defeat on Chris Wilder’s team.
Hope put the Shakers in front after only 14 minutes and Danny Mayor doubled it with a deflected strike 20 minutes later.
Substitute Daniel Rose sealed a comprehensive 3-0 win when he tapped in after an awful mix-up at the back.
Northampton created almost nothing of their own and fully deserved the loss, which means they remain firmly in the Sky Bet League Two relegation zone.
Wycombe’s 0-0 draw at Scunthorpe means they edge a point away from Town, while Portsmouth’s 2-1 victory at Newport County has extended their advantage to five.
But while results elsewhere were not favourable to the Cobblers, their own performance was not worthy of a win and will renew doubts about the team’s ability to stay up this season.
In glorious spring sunshine, Northampton were dealt a blow when Gregor Robertson was injured in the warm-up.
Ian Morris replaced him in the starting 11 but Chris Wilder was forced to abandon the wing-back system he had prepared the side for in favour of a conventional 4-4-2.
Marquis was always going to play and was sharp on his return, producing the game’s first shot with an admittedly tame effort from 25 yards.
His next attempt was a scuffed one on the run after Jim McNulty had hesitated in the heart of the visiting defence.
Bury took the lead when Daniel Nardiello reached the byline on the left wing and crossed for Hope to head powerfully home via the underside of the crossbar.
The response was good as Marquis hit the inside of the post after an intelligent Ian Morris backheel put him through but 20 minutes later Bury had doubled their lead.
Danny Mayor cut inside off his left wing and struck a shot with his right foot that deflected and looped over the stranded Matt Duke.
They should have had a third not long afterwards when Hope completely failed to connect with a near-post header after Craig Jones had crossed from the right.
And no stage did the Cobblers look like getting back in the game and in fact it was Bury who came closest to the game’s next goal when substitute Daniel Rose saw his firm shot well blocked by Duke.
Their best chance fell to Gary Deegan, who threw his left foot at long Ben Tozer throw only to see Brian Jensen instinctively stop it on the line.
Injury-time salt in the wound was applied by Rose, who was left with the simple task of tapping into an empty net after a calamitous piece of play at the back.
Horwood chipped a pass back to the keeper, who swung and missed with his clearance to present Rose with a free run at an unguarded goal.
Cobblers: Duke, McSweeney, Doumbe, Diamond, Horwood, Hackett, Ravenhill, Carter, Morris, Marquis, Sinclair
Subs: Dickenson (for Hackett 46), Deegan (for Ravenhill 46), Tozer (for McSweeney 71)
Not used: Moyo, Snedker, Connell, Toney
Bury: Jensen, Veseli, Mills, McNulty, Hussey, Jones, Sedgwick, Tutte, Mayor, Nardiello, Hope
Subs: Procter (for Mayor 51), Rose (for Nardiello 68), Platt (for Hope 72)
Not used: Cameron, Soares, Charles-Cook, Obadeyi
Away fans: 406