The hosts were stunned when Dejan Damjanovic scored on the stroke of half-time.
Team-mate Stevan Jovetic missed a golden chance to make it 2-0 when his scuffed penalty was saved by keeper Andriy Pyatov.
The referee pointed to the spot after Evhen Selin fouled Miodrag Dzudovic 10 minutes from time, the Sun informs.
Ukraine defender Oleksandr Kucher and Montenegro keeper Mladen Bozovic were booked for brawling during a break in play.
The home side were without coach Oleg Blokhin — who is set to take charge of Dynamo Kyiv — after he had an operation last week to treat thrombosis.
Montenegro have seven points from three games — the same as England.
Serhiy Dadu smashed home a 73rd-minute spot-kick for Moldova’s first goal of these qualifiers as they beat San Marino 2-0.
The tiny nation leap-frogged giant neighbours Ukraine in Group H with two late strikes.
Dadu coolly converted his spot-kick just two minutes after coming on as a sub following Lorenzo Buscarini’s clumsy foul on Vitaliy Bordiyan.
The Moldovans had more than 25 shots at goal and enjoyed an astonishing 84 per cent of possession.
But it was not until Alexandru Epureanu headed in Arthur Patras’ 78th-minute corner that the result was sealed.
Matteo Vitailoli came close to giving San Marino a goal to celebrate in added time but his shot from distance was saved by Stanislav Namasco.
San Marino remains bottom of the group with no goals and no points.
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