Chief Minister Jagadish Shettar had forwarded the resignation for acceptance, a Raj Bhavan communique said here.
Vallyapure, a staunch supporter of KJP leader B S Yeddyurappa had quit BJP on Saturday to join the new party.
The present strength of the Shettar led BJP ministry has come down to 32 from 34 in the wake of sacking of B J Puttaswamy, another loyalist of Yeddyurappa, and the resignation of Vallyapure.