Mukherjee was the President from 2012 to 2017.
The 83-year-old's political career spanned about five decades, during which he held various key posts in the Congress as well as in the governments of Indira Gandhi, Rajiv Gandhi, P V Narasimha Rao and Manmohan Singh.
Deshmukh, a Sangh ideologue, was a social activist and had been honoured with the Padma Vibhushan earlier.
Born in Hingoli in Maharashtra on October 11, 1916, he passed away in Satna in Madhya Pradesh on February 27, 2010.
Hazarika, who hailed from Assam, was a playback singer, lyricist, musician. He was born on September 8, 1926 and passed away on November 5, 2011.
Soon after the Rashtrapati Bhavan announced the award, Prime Minister Narendra Modi paid tributes to all the three.
"Pranab Da is an outstanding statesman of our times. He has served the nation selflessly and tirelessly for decades, leaving a strong imprint on the nation's growth trajectory. His wisdom and intellect have few parallels. Delighted that he has been conferred the Bharat Ratna," Modi tweeted.
For Hazarika, the Prime Minister tweeted, "The songs and music of Shri Bhupen Hazarika are admired by people across generations. From them radiates the message of justice, harmony and brotherhood. He popularised India's musical traditions globally. Happy that the Bharat Ratna has been conferred on Bhupen Da."
In another tweet, Modi said, "Nanaji Deshmukh's stellar contribution towards rural development showed the way for a new paradigm of empowering those living in our villages. He personifies humility, compassion and service to the downtrodden.
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