A pre-contract agreement has been reached for the 23-year-old to join Spurs when the transfer window re-opens in January, subject to a work permit being granted.
Khumalo, who impressed manager Harry Redknapp during a trial in September, will boost Tottenham's defensive options in what has been an injury-hit season for the club to date.
Spurs have taken advantage of the long-term partnership established with SuperSport United three years ago to bring Khumalo to White Hart Lane.
Speaking last month, Redknapp said of the player: "He's not expensive. We had him over on trial and we like him. He's got potential and we've got a tie-up with the club SuperSport so we've taken him on.
"It will be a great chance for the kid. He's a great lad. He comes from a poor background and he's desperate for a chance, and we're going to give him a chance."
Khumalo played in all three of South Africa's matches at their home World Cup during the summer, scoring in the 2-1 victory over France.
Rumours linking him with Spurs began shortly after the tournament, with the defender saying at the time: "I have always wanted to play in England and obviously in the Premier League, and it would be a dream to move to Tottenham.
"Playing in the Champions League would be another dream.
"I think the Champions League is the closest level to the World Cup in terms of quality and the play, so it would be great to make the move."
Source: PA
Source: PA