Memphis Depay gave the Netherlands a 2-0 lead but Montenegro came from behind with Ilija Vukotic and Nikola Vujnovic in the 82nd and 86th minutes at Podgorica City Stadium.
The Netherlands could have earned a spot in the World Cup if they had beaten Montenegro but now the race to qualify heats up in Group G with one match left to play.
Having collected 20 points, the Netherlands still top the group and have a huge advantage to directly qualify for World Cup. They are followed by Turkey and Norway with 18 points each.
Turkey are in the second spot on goal difference after beating Gibraltar 6-0 at home.
Montenegro are in fourth place with 12 points.
Latvia increased their points to six and Gibraltar sit at the bottom of the table with zero points.
The Netherlands and Norway will face off, while Turkey will visit Montenegro in the last group matches.
Group leaders will automatically qualify for the tournament while the second-place team will head to the playoffs.
France, Belgium secure spots at FIFA World Cup in Qatar
France hammered Kazakhstan 8-0 on Saturday to qualify for the 2022 World Cup as Belgium also earned a spot.
Kylian Mbappe was impressive for France -- scoring four goals. Karim Benzema netted twice, Adrien Rabiot and Antoine Griezmann each contributed to the defending champions' easy win at Parc des Princes.
France lead Group D with 15 points. Finland increased their points to 11 after beating Bosnia and Herzegovina 3-1 in an away match.
Ukraine have nine points and is in the third spot.
Belgium booked a place in Qatar with a 3-1 win against Estonia at home in Group E.
Goals from Christian Benteke, Yannick Carrasco and Thorgan Hazard gave Belgium the easy win while Erik Sorga was the lone scorer for the visitors.
Having collected 19 points, Belgium now tops the group with 19 points, five points ahead of Wales, which secured a playoff spot.
