Radomir Djalovic put the home side in front eight minutes after the break with a fine left-footed volley from a pinpoint left-wing cross from Vladimir Bozovic.
They were denied victory when Bulgaria striker Ivelin Popov scored from close range midway through the second half - the first goal have conceded in the campaign.
Bulgaria survived a few nervous as Savo Pavicevic hit the post with a 20-metre shot and Marko Basa headed against the bar from Nikola Drncic's corner.
"I was very angry with our first half performance and I let the lads know about that in the dressing room at the break," Bulgaria coach Lothar Matthaus told Bulgarian state television.
"But we played well in the second half and I was pleased with it. We still have a slim chance (to reach the finals) and we'll fight until the very end but we know we have to work and prepare the team for the World Cup's qualifiers."
Despite the setback Montenegro, who failed to win a single game during the 2010 World Cup qualifiers, are still in a good position to qualify for next year's tournament.
England, who salvaged a 2-2 draw with Switzerland after trailing 2-0 at Wembley, top the group from Montenegro on goal difference with 11 points from five games.
Montenegro host England on October 7.
