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Brechin had a goal disallowed when Stevie Hampshire rose above the keeper to nod into the path of Grant Johnson who prodded into the net, but the ref disallowed the goal for a foul on Saint's keeper' Kevin Cuthbert.
St Johnstone opened the scoring against the run of play in the 18th minute when Chris Hay's shot was parried by Davie Hay right back into his path and he made no mistake from the rebound.
Just before half time, Brechin were inches away from opening the scoring when Ally Mitchell's full volley straight from Charlie King's corner cannoned off the cross-bar, it just summed up Brechins luck this season.
Referee Brian Cassidy had to go off at half time as he had picked an injury and was replaced by Linesman Willie Gillfillan, and St Johnstone fan John Dobbie ran the line for the second half.
The points were selaed for St Johnstone just before the hour mark when Davie Hay failed to control a passback and Baxter pounced to score.
Brechin's misery was complete when Charlie King had to be stretchered off and has suspected ligament damage and could be out for some time.
Attendance: 822
Referee: Brian Cassidy, Cumnock
BCR's MoM- Most of the Brechin players had a poor game but Ally Mitchell wasn't scared to get stuck in and almost opened the scoring just before half time from a breath-taking volley.
Brechin City: Hay, Millar, Dowie, Smith, McCulloch, King, Johnson, Winter, Mitchell, Templeman, Hampshire. Subs: White, McLeish, Gibson, Deas, Budinauckas.