Paulo Fonseca's side had not won away from home in the league since late October but moved within a point of their hosts thanks to Bruno Moreira's goal 13 minutes before half-time.
When Hugo Ventura raced out of goal to clear a loose ball, the Pacos forward chased him down and got lucky when the clearance struck him and deflected back over the hosts' goalkeeper.
When the ball eventually landed just yards outside an open goal, Moreira had the simple task of nodding home what proved to be the winner.
Belenenses and Pacos now sit six and seven points off the final European qualification place currently occupied by Vitoria Guimaraes.
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