The party said it had come to the conclusion that the nomination form was rejected due to gross negligence on his part or "in connivance with the BJP."
The second phase of Lok Sabha polls involves 88 constituencies across 13 states and union territories. Polling was held for 102 seats in the first phase on April 19.
Bengaluru South MP booked for violating the Model Code of Conduct after posting a video of the Ayodhya Ram Temple on social media on Thursday, allegedly seeking votes using religion.
Shah alleged that for the Congress, Muslims have the first right over the country's resources, but for the BJP, the poor, Dalits, OBCs, and tribals have the first right.