There was a six-minute delay between the fall of India's second wicket and the arrival on the field of Sourav Ganguly.
As the delay lengthened there were boos from the crowd, while the South African players asked umpires Daryl Harper and Asad Rauf about the "timed out" rule whereby a batsman can be given out if he is not ready to face within three minutes of the previous wicket falling.
Cricket South Africa media officer Gordon Templeton said the explanation from match referee Roshan Mahanama of Sri Lanka was that Tendulkar had been ready to bat at his usual position of number four.
But because he had been off the field for 18 minutes at the end of the South African innings the previous day he was not permitted to bat until the same amount of time had elapsed at the start of India's innings.
With India losing their first two wickets within 12 minutes of the start of play Tendulkar could not bat.
"The match officials worked out that Sachin could only come out to bat at 10.48am," said Templeton.
"The fourth official (South African umpire Murray Brown) only made it to the Indian dressing room the ball before (second man out) Wasim Jaffer was out."
With Tendulkar not permitted to bat, Ganguly had to get ready instead.
"According to the rules, Sourav Ganguly could have been timed out but because of special circumstances in that the fourth official got to the dressing room late he was not timed out," said Templeton.