Nagar resigned as the minister for Dairy, Khadi and Rural Industries after the woman lodged an FIR against him alleging he raped and assaulted her at his official bungalow on September 11 after taking her there on the pretext of giving her a job.
"Babulal Nagar stands suspended from Congress with immediate effect," AICC General Secretary in-charge Rajasthan, Gurudas Kamath, told PTI.
He said the AICC has intimated the Pradesh Congress Committee of Rajasthan through a written communication this evening.
53-year-old Nagar has denied the charges, saying that his political rivals were trying to "frame" him ahead of Assembly elections in the state.
A medical board had examined him and collected his semen and other samples for forensic tests after Nagar reported at the hospital unescorted by CID-CB sleuths, who reached there separately.