The two parties, constituents in the state government, had mounted an acrimonious campaign for the Palghar Lok Sabha bypoll which was held on May 28.
The BJP won the seat with its candidate Rajendra Gavit defeating Sena's Shrinivas Wanaga by a margin of 29,572 votes.
"Fadnavis asked the party's state office-bearers to try for a pre-poll alliance with Shiv Sena. But, he said that if the alliance does not materialise, we should prepare to contest alone," Raosaheb Danve, the BJP's state unit chief told reporters here.
The Sena, however, has stated several times in the past few months that it would contest all future polls alone.
The resolution to part ways with the BJP and go for it alone in the Lok Sabha and Assembly polls next year was tabled and passed unanimously at Sena's National Executive meeting held in January this year.