The accused, identified as Samsher Khan (25) and Ravi Solanki (28), were arrested from Wadala and Tunga, respectively, police said, adding that both were drug addicts.
The body of the four-year-old girl had been found near MTNL office at Tunga.
She had gone missing from her house in the village on the night of March 6 and her parents had lodged a complaint.