Konoplyanka tried his luck again five minutes later, but this time his drive flew high over the crossbar as the hosts threatened to take the lead.
Despite that opportunity, Ukraine should have taken the lead with 36 minutes played as Andriy Yarmolenko shook off his marker to head over from six yards out.
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However, the home side finally opened the scoring in stoppage time when Sergiy Sydorchuk fired in from close range after being picked out inside the box by Yarmolenko.
Ukraine had a glorious chance to double their advantage at the start of the second half when they were awarded a penalty for Aleksandar Damcevski's foul on Roman Zozulya. Yarmolenko stepped up to take the resulting spot kick, only to smash the ball against the crossbar.
Chances then fell to Artem Fedetskiy and Sydorchuk, though both players failed to hit the target as Ukraine pushed for a second goal.
Macedonia's best opening came with 15 minutes left on the clock, only for Jovan Kostovski to head wide from about six yards out.