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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.
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.