Mukherjee placed a wreath near the casket containing the body of Jayalalithaa at the Rajaji Hall here.
Mukherjee was accompanied by Tamil Nadu and Maharashtra Governor Ch Vidyasagar Rao.
Meanwhile, Jayalalithaa's mortal remains have been shifted from Rajaji Hall and put on a flower-decked cortege for burial at MGR Memorial.
Earlier this morning, an Indian Air Force plane carrying President Mukherjee to Chennai for the funeral of Jayalalithaa returned mid-way due to a snag, delaying his arrival in the state capital.