The woman in her 70s was seriously injured in the attack at the Convent of Jesus and Mary School in West Bengal state on March 14.
A group of thieves entered the building tied up the school's security guards and then entered the nun's room.
Before leaving they destroyed the chapel and stole cash and laptops.
Police said the suspects were arrested after a nationwide hunt.
One was found hiding in the western city of Mumbai and the second in West Bengal state.
Officers told reporters one of the accused, Mohammad Salim Shaikh, denied the rape charge but accepted he was involved in the break in.