Khumalo impressed during a trial at Spurs last July and the north London club have chosen to take the 23-year-old on a permanent transfer for a fee of around £1.5million.
The centre half, who was born in Swaziland, impressed for South Africa during the World Cup where he scored the opener in the hosts' 2-1 group stage win over France.
Spurs boss Harry Redknapp already has a number of options in defence but there are still doubts over the long-term fitness of centre backs Ledley King and Jonathan Woodgate.
Khumalo could make his debut in Tottenham's FA Cup third round clash with Charlton at White Hart Lane on Sunday.
Source: PA
Source: PA