Wagh was brought here by local police from Mumbai at 2 am, and was admitted to Nashik civil hospital as he complained of ill-health, police said.
Wagh represents Pachora in neighbouring Jalgaon district. The NCP had yesterday suspended him from the party following the charges.
Mali was picked up by Sarkarwada police here, sources said.
A 20-year-old girl from Pathardi, Ahmednagar district, had alleged that Wagh and Mali called her to Nashik, promising to give her a job, and raped her on February 21 at the Government guest house here.
She lodged the FIR on February 25. According to her complaint, she first met Wagh in Aurangabad, where the MLA promised to arrange a job for her.
The girl has undergone a medical test, following the complaint, which confirmed sexual intercourse with her, police said.
Wagh had alleged that it was a "political conspiracy" to frame him.
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