"We have discussed topical issues, including the forthcoming referendum," Vujanovic told reporters in St Peter's Square.
Also discussed were relations between the Catholic and the Orthodox faithful in Montenegro, which Vujanovic described as excellent.
The talks were held in the pontiff's private library in the English language and without interpreters.
Vujanovic presented the pope with a copy of the accords which Montenegro signed with the Vatican in 1876, and invited him to visit Podgorica.
The pope told Vujanovic that he wished a peaceful future for his country.
Vujanovic also discussed the planned referendum with the Holy See's State Secretary, Angelo Sodano, who said that the Vatican would harmonise its views on the matter with those of the European Union.
The visit of the Montenegrin head of state to the Vatican was organised by the Knight of the Maltese Order, Anto Zbutega, who is of Montenegrin descent.