Bhatt, who was an external expert on the Search and Selection Committee (S&SC), resigned with "immediate effect" as "there may be a potential conflict of interest", the bank added.
Bhatt is under CBI's scanner in connection with loans given to the now defunct Kingfisher Airlines, promoted by fugitive liquor baron Vijay Mallya.
On Tuesday, Yes Bank's non-executive chairman Ashok Chawla had resigned as his name figured in a CBI chargesheet filed in the Aircel-Maxis case.
"The Nomination & Remuneration Committee ('NRC') of the Bank while accepting Mr. Bhatt's resignation has recognised his guidance and inputs during his association with the S&SC as an External Expert," Yes Bank said.
The bank further said that given the significant progress made by the S&SC with the support of Korn Ferry over the past three meetings (most recent being held on November 13) in its mandate to identify a suitable successor to Kapoor, the NRC has decided to continue with the existing members to complete the process as per the timeline communicated by RBI.
The Reserve Bank of India (RBI) has asked the private sector lender to find a replacement for its founder MD and CEO by January 31.
Last month, Yes Bank had said the search panel had finalised the potential candidate profile.