The West Bengal Chief Minister displayed the victory sign after exercising her franchise at the state Assembly.
Banerjee, who had opposed the candidature of Mukherjee, announced her party's support for him on July 17, after keeping up the suspense for nearly a month.
Railway Minister Mukul Roy also cast his ballot along with the Trinamool Congress supremo.
Leader of the Opposition Suryakanta Mishra, belonging to the CPI(M), also cast his vote.
Meanwhile, Mukherjee's son Abhijit, a Congress MLA from West Bengal, was all praise for the Trinamool Congress for its decision to vote for his father.
"It is all the more pleasant for me that the Trinamool Congress, which is the major ruling party in West Bengal, decided to vote in favour for the UPA candidate. It is also a matter of satisfaction that my father will be getting the maximum votes from his home state," Abhijit said after casting his ballot in the Assembly.
Abhijit said there was rare unity in Bengal when almost all political parties showed solidarity in backing his father.
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"It is a rare unity to vote together in the interest of Bengal. If such solidarity is maintained, it will be beneficial for Bengal's development and to get more assistance from the central government," he said.
CPI(M) and Forward Bloc have announced their support for Mukherjee, while two other Left Front constituents - CPI and RSP, have decided to abstain from voting.
Confident of his father's victory, Abhijit said he would hold a family get together in Delhi after July 25.