Fatos Beciraj volleyed Montenegro ahead in the 38th minute from Jovetic's cross and the pair combined again early in the second half when Beciraj provided the cross for the Inter Milan forward to control and fire home.
Jovetic has found a new lease of life since joining Inter on loan from Manchester City, scoring three goals in his first two Serie A games this season.
Montenegro are fourth in Group G with eight points, three behind Russia, and still have an outside chance of clinching third place which earns a two-leg playoff for a place in France.
However, they would have to beat Russia away and hope the Russians drop further points in their remaining games to have a realistic chance.
Liechtenstein are fifth with five points.
(Writing by Brian Homewood in Berne; editing by Toby Davis)
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