Sri Lanka captain Mahela Jayawardene fell for 374, 26 short of Brian Lara's Test record but did share in a new landmark on an amazing day in Colombo.
Jayawardene set a new partnership record of 624 with Kumar Sangakkara, who hit 35 fours in 287.
The skipper continued, but one short of Lara's second highest score of 375 and six behind Matthew Hayden's 380, he was bowled by one that kept a touch low.
Sri Lanka declared on 756-6, with South Africa closing 544 adrift at 43-0.
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The third-wicket pair surpassed the previous best of 576 for the second wicket by fellow Sri Lankans Sanath Jayasuriya and Roshan Mahanama against India at the nearby Premadasa stadium in 1997.
Jayawardene made his debut in that match, in which the Sri Lankans posted the highest Test team score of 952-6.
The skipper was on 278 and Sangakkara was on 273 when they set the new record in the second over after lunch on the third day at the Sinhalese sports club.
Ironically the pair had come to the crease on Thursday evening with Sri Lanka struggling at 14-2 and Sangakkara had a reprieve when he was bowled off a no-ball before he had reached double figures.
Both batsmen batted for more than 10 hours, or 160 overs, in hot and humid weather in the Sri Lankan capital.
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Neither offered a chance before Sangakkara's dismissal on day three, with an lbw appeal by Makhaya Ntini against Jayawardene and a streaky edge through the slips by Sangakkara the closest South Africa came to dismissing them.
Had Sangakkara completed a triple century it would have been the first time in a Test innings that two had been scored, but he was caught off the outside edge driving at Andrew Hall.
Tillakaratne Dilshan, who had to wait for 11 hours of match time to come in at number five, hit a rapid 45 to help add another century with his captain, who declared immediately after his marathon innings was ended by Andre Nel.