Representing the government and the people of India, Mukherjee, one of the few foreign speakers to give their eulogies at the memorial service for the anti-apartheid icon, said "we stand by you in your hour of bereavement and we share your sense of loss today".
Accompanied by a high-level delegation including UPA chairperson Sonia Gandhi and leader of opposition Sushma Swaraj, the President flew in early this morning to join South Africa in paying homage to 'Madiba', as Mandela was affectionately called.
The FNB stadium, where Mandela had made his last public appearance a few years ago, reverberated to a standing ovation when Mukherjee made his entry and his name was called out.
For India, Mukherjee said, the passing away of Mandela represents the departure of the venerated elder, a great soul.
"We pray for his eternal peace. Madiba lived a life of sacrifice and privation as he pursued a seemingly impossible goal for his people - and the world is richer for his legacy.
"We, in India, have long admired him - and all that he stood for - and we will always cherish his friendship and love for our people," he said.
The President described Mandela as a visionary who epitomised and an uncommon humaneness that inspired all of mankind.
"We have no doubt that the world will honour the historic legacy of Madiba, one of the most influential personalities of our century, who taught the world the true meaning of forgiveness and reconciliation - and steered South Africans onto the path of building a truly Rainbow Nation," he said.
Mukherjee said Mandela was an icon of irreversible social and economic change - the kind of transformation and emancipation that his people had only dreamt of.
"A towering personality of great compassion and wisdom, he guided his nation, bruised by decades of apartheid and violence, to embrace his simple message of tolerance and harmonious co-existence.
"Indeed, his life and struggles - which represented 'hope' for the downtrodden in South Africa and all over the world, remind us of the principles that the father of our nation, Mahatma Gandhi, stood for," he said.
Mukherjee said in the face of the severest persecution, punishment and relentless oppression, Mandela continued his non-violent struggle with dignity and pride, refusing to be intimidated.
"He never diminished his commitment to his kind of 'satyagraha' against injustice and inequality. His stoic determination, patience and magnanimity reminded us, in India, of the revolutionary methods of Mahatma Gandhi," he said.
He said it was, therefore, an honour for Indians to confer upon Mandela the highest civilian award - Bharat Ratna - when he visited India in 1990. He received an unprecedented welcome and was felicitated in Delhi and Calcutta.
The President recalled that in 1995, when he visited India as the first President of post-apartheid Africa, Mandela visited Gandhiji's Sabarmati Ashram and said that it was for him a homecoming, a pilgrimage.
"We, on our part, associate South Africa with the first chapter of Mahatma Gandhi's freedom movement. Gandhiji had staked his career as a budding lawyer in South Africa to resist segregation and inequality - before he embarked for India and took up, in India, the same cause," he said.
Mukherjee said that the six principles that Madiba identified as the fundamentals of the foreign policy of the new South Africa are the same principles that the founding fathers of free India had enshrined in our own policy of Panchsheel.
He said Mandela often acknowledged the influence of Mahatma Gandhi and the first Prime Minister of India , Jawarharlal Nehru, on his own thought process.
"It is no wonder then that we, in India, attach great sentiment to our unique friendship with the people of South Africa," he said.
"We stand by you in your hour of bereavement and we share your sense of loss today," he said.