Thackeray also said that he had also contacted Singh, Sushma Swaraj and party patriach L K Advani during the talks with BJP on the seat-sharing and apprised them about the situation.
"I had told Rajnath Singh to continue as BJP President till Maharashtra elections. Had he been there, he would have kept us together.
"A day before BJP parliamentary board decided to nominate Modi as PM candidate, he had called me to tell me that his name will be announced and sought our support. I supported it. He is someone who can keep things together," Thackeray told news channels.
"I had even called Advaniji to tell him what is happening and even he said that it won't be good if the alliance breaks. I told him that please forgive me if the alliance breaks," he added.
Thackeray said the way Shah spoke about a rally in Kolhpaur about having the next BJP government in Maharashtra, it was evident that BJP did not want Shiv Sena as ally.
"The way Amit Shah made the speech in Kolhapur, the way they were talking it was becoming clear that now they don't want us," Thackeray said.
The Sena leader said even earlier there were instances when there was a strain in the alliance but the "mature" leaders like late Pramod Mahajan and Gopinath Munde knew how much to strech.
"My intention was never to break the alliance. When Mahajan and Munde and we were handling alliance issues, things were good. When Delhi-appointed people came in and started doing negotiations, things went wrong.
"Amit Shah told me Om Mathur (BJP leader) has been appointed to conduct negotiations. Mathur said we have been told by the parliamentary board to get equal or nothing. I told them that BJP's parliamentary board can decide your seats not mine," he said.
Speaking on the issue of resignation of lone Sena minister in Narendra Modi's cabinet Anant Geete, he said he will speak to the Prime Minister about this.
"I never made issues about only one cabinet in the government. Why should we resign? When Modi returns, I will speak to him," Thackeray said.