Danny Whitaker put the home side ahead with 10 minutes played but goals from David Syers and James Hanson either side of half time turned the game around before Bowery had the last word with a low finish in added time.
Rotherham got their promotion push back on track - and Adam Le Fondre re-found his goal touch - in a 4-0 win over Stockport.
Rotherham romped to a three goal lead in just 34 minutes after a 10th-minute own goal by Aaron Brown, and neat strikes from Le Fondre and Ryan Taylor.
The hosts' fourth came in the 57th minute, and owed a great deal to Le Fondre. He chased a lost cause to the by-line, the defender failed to put the ball out and Le Fondre crossed for Taylor to fire home his second.
Striker Ashley Grimes grabbed a late winner for Lincoln to send Port Vale tumbling to a 1-0 defeat.
Grimes found the net three minutes from time when he fired in from 10 yards after a surging run from Josh O'Keefe opened up the Vale defence.
The result lifted Lincoln clear of the relegation places giving manager Steve Tilson his third win in eight days.
Barnet were plunged deeper into the League Two relegation battle, however, as Barry Corr wrapped up the points in a 2-0 win for Southend.
Anthony Grant had given the Shrimpers the lead after 25 minutes before substitute Corr smashed home a second after the break following a comedy of errors in the Barnet defence.
Goalkeeper Liam O'Brien's loose pass was intercepted by Ryan Hall who calmly squared the ball for Corr to hammer into an open net.
Goalkeeper Ryan Clarke brilliantly saved a penalty 10 minutes from time to earn Oxford a point in a 1-1 draw with Cheltenham.
The Robins led from Thomas' chip over Clarke in the 26th minute, before Tom Craddock hauled Oxford level seven minutes later with a low header.
Anthony Tonkin then fouled Brian Smikle in the box on 80 minutes, but Clarke's full-length dive to his right-hand post kept out Wes Thomas's spot-kick and handed Oxford a point.
The 24-year-old joined on a season-long loan in the summer as part of the deal that took Simeon Jackson in the other direction on a permanent deal.
But the Gills faithful have hardly missed their former hero thanks to McDonald and the ex-Dartford man struck twice in the second-half to keep his side in the play-off places.