"I won't accept this as a defeat because the BJP used 'saam, daam, dand, bhed' (request, money, punishment and division) to win," said Shiv Sena chief Uddhav Thackeray.
Despite being part of the ruling coalition in Maharashtra the two parties have often traded charges against each other, with the Sena openly taking on the central government as well.
Another front was opened in the uneasy ties when the Shiv Sena fielded the son of BJP lawmaker Chintaman Wanga whose death necessitated the bypoll. The decision led to sharp remarks from BJP leaders, including Maharashtra Chief Minister Devendra Fadnavis.
While the Shiv Sena accused the BJP of betraying the Wanga family, UP Chief Minister Yogi Adityanath, during a rally in Palghar last week, said Shiv Sena had "back-stabbed" the BJP.
The Sena president hit back on a day the BJP lost the Kairana Lok Sabha seat in Uttar Pradesh to a united opposition. "People have taken away Yogi (Adityanath's) glee."
After losing three seats in three months, the BJP's tally of elected members in Lok Sabha is now down to 272, as opposed to 282 seats it won in 2014.
"When BJP came to power in 2014, we thought this government is here to stay for at least 25 years. But after four years, they are losing most by-elections, which has reduced them to a minority now," mocked Mr Thackeray.
The BJP reacted with caution. "We respect the Shiv Sena It has the freedom to speak," said BJP spokesperson Sambit Patra.
The Shiv Sena also targeted the Election Commission over the malfunctioning of vote machines in the just concluded bypolls. Unless the controversy is resolved, all political parties should consider boycotting elections, said Mr Thackeray.