Sanader spoke to Djukanovic on the telephone during his visit to Macedonia, the Croatian government's public relations office said in a statement.
The Croatian PM congratulated Djukanovic on the organisation of the vote and its democratic atmosphere.
He added that Montenegro had shown a high level of democratic maturity and determination to gain international personality and independence.
Croatia respects that fact and will recognise Montenegro as a new member of the international community, Sanader said.
The two prime ministers said the process of disassociation of Montenegro and Serbia had to be conducted in the spirit of tolerance and mutual respect, adding that both countries had opted for integration with European associations, which Sanader said Croatia would fully support.
Djukanovic thanked Sanader for his congratulations, the statement said.