Following an untidy start at the Nacionalna Arena Filip II Makedonski, Juan Mata edged into space just outside the penalty area and swung a ball goalwards which deflected off Pacovski and into the net.
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Diego Costa threatened three minutes later after making a yard for himself inside the box and sending an effort just wide of the left post, but the hosts countered through Milovan Petrovic, whose shot in the area sailed well over.
Spain goalkeeper David de Gea was untested until just before the half-hour mark, when Leonard Zhuta broke down the left and curled a cross in from the flank, which was nonchalantly plucked out of the air by the Red Devils goalkeeper.
In what turned out to be a largely tame first half, La Roja had the final say before the break through Dani Carvajal, who received a neat pass on the edge of the penalty area, but his first-time drive rattled the Macedonia crossbar before Juan Bernat's rebound was held by Pacovski.
Macedonia weighed in with the first chance after the restart when Ferhan Hasani lashed a free kick narrowly over the crossbar from the edge of the box, with De Gea stranded.
Ljubinko Drulovic's side, well drilled in defence, continued to frustrate their more illustrious opponents, keeping them from recording any meaningful shots on goal - even when Paco Alcacer fired home in the 71st minute, the referee called it offside.
This would matter little because Macedonia, for all their defensive qualities, were unable to cause much trouble in attack, and Spain were thus able to see the game out and clinch all three points.
The result means that the incumbent European champions have established a two-point gap at the top of Group C between themselves and second-placed Slovakia, while Macedonia prop up the table.