Mukherjee submitted his resignation to Prime Minister Manmohan Singh, who told him that his presence "amidst us" would be deeply missed as "our government owes a deep debt of gratitude to you for your contribution."
The 77-year-old veteran Congress leader, who is the UPA candidate for the July 19 Presidential poll, left the Finance Ministry after an over three-year stint which saw highs and lows of the Indian economy.
The Prime Minister decided to keep the Finance portfolio with himself at a time when the economic difficulties have surmounted with the GDP growth on a downslide and value of rupee declining.
Mukherjee, the Leader of the Lok Sabha who was the UPA government's trouble-shooter, is expected to file his nomination papers on Thursday.
"I stand ready to embark on a new journey," he said as he left his North Block office to tender his resignation, profusely thanking the media and all others for their support.
In his last message as the Finance Minister, he said he felt "honoured" and "humbled" on being nominated by UPA as a candidate to contest the Presidential election with support from SP, BSP, JD(U), Shiv Sena, CPI-M, Forward Bloc and some other parties.
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One of the UPA constituents Trinamool Congress has so far not committed support to his candidature.
"Yet, standing on the brink of such an honour, I will also feel a pinch of sentiments at the thought of leaving behind my life as a political activist, spanning over four decades," he said.