Yechury also questioned the "mind-boggling" speed with which the decision was taken.
"Like Ceasar's wife, the Rajya Sabha Chairman's decision must be above questioning, but the disqualification of Rajya Sabha MPs Sharad Yadav and Ali Anwar casts a shadow," Yechury tweeted.
He also questioned the urgency shown by the chairman.
"The petition was filed on September 2 and the decision is out on December 4. The speed is mind-boggling. Similar cases are pending in Lok Sabha for over a year. So political affiliation is the only thing that matters?" the Left leader asked.
Naidu said in his communication that both leaders ceased to be Rajya Sabha members with immediate effect.
He agreed to the JD(U)s contention that the two senior leaders had voluntarily given up their membership by defying their partys directives and attending events of opposition parties.