Midfielder Arda Turan, likely to be key to Turkey's prospects in France, set up the goal with a well-flighted cross in the fourth minute of stoppage time and Topal charged into the area to head beyond the diving Montenegro keeper.
Until that moment the visitors had contained the threat from Turkey well, playing in a packed stadium in Antalya on Turkey's Mediterranean coast.
Hakan Calhanoglu, who scored Turkey's first ever goal for Turkey against England in last Sunday's 2-1 defeat, went close in the seventh minute with a powerful shot from outside the area which flew over the bar.
Turkey had further chances through Volkan Sen and Oguzhan Ozyakup but both fired wide.
Montenegro continued to absorb pressure in the second half until Arda managed to cut open the defence.
Before last week's loss to England, Turkey had been undefeated in their previous 14 games, having qualified for the European Championship with an impressive late burst.
Turkey face holders Spain, Croatia and Czech Republic in their group in the month-long European Championship finals which start in France on June 10.
