The monarch and her husband joined senior politicians and troops on Horse Guards Parade to greet the leader as he began his state visit to the UK capital.
After the Band of the Grenadier Guards played the South African national anthem, Mr Zuma and Prince Philip inspected 101 men of Nijmegen Company.
A traditionalist Zulu, the 67-year-old statesman's lifestyle has been the subject of some controversy.
He has three wives, the newest of whom, former bank clerk Thobeka Madiba, 36, is accompanying him on his trip. He also has 20 children born both in and out of wedlock.
After a private lunch with the Queen at Buckingham Palace, Mr Zuma travelled to Muswell Hill to unveil a plaque at the former home of Oliver Tambo, the man who helped Nelson Mandela found the modern South Africa.
On Wednesday night the Queen will host a state banquet in his honour, while he's set to hold talks with Prime Minister Gordon Brown on Thursday before meeting Prince Charles at Clarence House on Friday.