A first information report (FIR) was registered against Nagar at the Sodala police station here Sep 19.
Nagar, 53, resigned from the state ministry two days after the FIR was registered.
"The All India Congress Committee (AICC) issued direction regarding his suspension from the party as he was facing serious charges," said a senior Congress leader in Rajasthan.
He said the Pradesh Congress Committee suspended Nagar late Monday evening in compliance of the directions.
The state government has also recommended a CBI probe into the case.
The Central Bureau of Investigation (CBI) is likely to take up the case in the next couple of days, sources said.
Sources did not rule out the possibility of Nagar's arrest soon after the CBI begins the investigation.
A medical examination was conducted on Nagar at the SMS Hospital here Saturday. Doctors took Nagar's blood and semen samples to match the DNA with that of samples lifted from the woman's clothes.
In her police complaint, the 35-year-old woman alleged that Nagar called her to his government residence on the pretext of giving her a government and raped her Sep 11.
Besides Nagar, two other legislators of the ruling Congress party, Malkhan Singh and Mahipal Singh Maderna, were also suspended in December 2011 following allegations of sexual exploitation and murder of government nurse Bhanwari Devi.
--IANS (Posted on 01-10-2013)