Clanfield suffered a second successive home defeat in a mistake-ridden Division '1' West game.
The visitors went ahead after just 35 seconds when Garth Walsh capitalised on a defensive error, but two and half minutes later, it was 1-1, Neil Barrett netting after a defender slipped.
Alan Webb put Malmesbury ahead again on 14 minutes, only for Chris Hunt to lash a 30-yard shot past Graham Jones.
Both sides were less ambitious in the second half with a breakaway on 65 minutes proving decisive. The experienced James Row easily eluded a retreating defence to slide home the winner.
* Bishops Cleeve 2, Middle Barton 1
Ian Frazer ended his goal drought, but Middle Barton still conceded two soft goals to finish pointless.
A goal early in each half sealed their fate, defensive errors again proving costly.
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