Mukherjee defeated his main challenger and former parliament speaker P.A. Sangma by more than 50 percent.
In his congratulatory remarks, Zuma said South Africa looked forward to engaging India at the highest level.
"South Africa will also explore new opportunities in both the bilateral and multilateral environments to engage India in an evolving global environment."
Noting that India is a strategic partner, the President said South Africa's objective will be to build on the strong bilateral relationship and continue to foster goodwill and sound relations across a broad spectrum.
The two countries are strategic partners at a multilateral level and have created a platform for cooperating in various forums, namely the Brazil, Russia, India, China, South Africa (BRICS) forum; the India, Brazil, South Africa (IBSA); the Brazil, South Africa, India, China - a climate change-specific forum; the G-20 and the India-Africa Forum, all of which reinforce the strong bilateral relationship between the two countries.
The 77-year-old Mukherjee will be sworn in as the country's President by the Chief Justice of India on Wednesday, succeeding the incumbent Head of State Pratibha Patil whose five-year term ends on the same day.
Mukherjee, who was nominated by the Congress-led United Progressive Alliance to contest the presidential poll held on July 19, has held key portfolios like defence and foreign ministries in his political career spanning over 43 years.
India's President is the ceremonial head of state and is elected by an electoral college, comprising Members of Parliament and state legislators.
