The Pilgrims, who made eight changes ahead of kick-off with an eye on their impending Emirates FA Cup trip to Rochdale, were beaten courtesy of Mike Brewster's 88th minute strike.

United's disappointing afternoon was compounded by a facial injury sustained by debutant defender Pierce Bird during the first half.

Only Peter Crook, Luke Shiels and Ashley Jackson started again following Tuesday night’s 2-0 win over Blyth Spartans.

Seven players were out of contention, with George Willis, Simon Ainge and Alex Penny injured, Demeaco Duhaney and Martyn Woolford suspended and Tom Clare and Karl Byrne cup-tied.

Nicky Walker blasted an early effort wide for the Pilgrims, while Bird turned an effort against the post following a deep Walker corner.

Atherton responded and Ben Hardcastle rattled the post in the hosts’ next attacking foray.

Jordan Adebayo-Smith teed up Shaun Tuton with some good footwork but the eventual shot flew into the side-netting.

Crook had to save well to thwart Vinny Bailey from distance before the Pilgrims lost the services of Bird due to a blow to the face.

Both Brewster and Tom Bentham fired efforts off target for the hosts before the break.

Crook had to be alert to deny Gareth Peet after half-time and despite dominating the ball in the second half, the Pilgrims struggled to carve out too many clear-cut openings.

Jay Rollins and Walker teed up Jake Wright, but his effort was saved by Greg Hartley in the Atherton goal and Tuton’s low drive was also stopped by the home keeper.

Atherton sealed an unlikely triumph two minutes from time when BREWSTER waltzed into the area to angle the winner past Crook.

There was still time for Jonathan Wafula to somehow head wide at the back post following Middleton’s deep cross as United’s FA Trophy hopes slipped away for another year.

Atherton (4-4-2): Greg Hartley; Clive Smith, Danny Lafferty, Niall Battersby (Danny Lambert 82), Gareth Peet; Ben Hardcastle, John Welsh, Mike Brewster, Ben Conway (Danny O'Brien 64); Tom Bentham, Vinny Bailey (David Sherlock 64). Sub (not used): Steve Kipre.

Boston (4-4-2): Peter Crook; Ben Middleton, Luke Shiels, Pierce Bird (Alex Whittle 32), Ashley Jackson; Jordan Adebayo-Smith (Jay Rollins 66), Jonathan Wafula, George Green, Nicky Walker; Shaun Tuton, Jake Wright (Jordan Thewlis 84). Subs (not used): Tom Platt, Brad Abbott, Dominic Knowles, Andi Thanoj.

Referee: Matt Corlett.

Attendance: 303.