Knowing that a draw in Colombo would be enough to secure a 1-0 series win, the tourists adopted an extremely cautious approach in order to avoid defeat.
Captain Hashim Amla followed up his first-innings 139, which spanned more than eight hours, with a 159-ball 25, while Vernon Philander finished unbeaten on 27 off 98 deliveries as South Africa, set 369 to win, closed on 159-8 from 111 overs.
Amla ended the match having faced 541 balls, the fourth-highest total by a South African, and his side are now back to number one in the International Cricket Council Test rankings at the expense of Australia.
Sri Lanka, meanwhile, will rue their failure to triumph in a game they dominated for large parts.
Although spinners Rangana Herath (5-40 from 45 overs) and Dilruwan Perera (3-60 from 44) did their best to force victory, South Africa were ultimately rewarded for their stubbornness.
The ninth-wicket pairing of Philander and Imran Tahir saw out 8.1 overs to deny Sri Lanka, the latter contributing four not out.
Despite two rain breaks, Sri Lanka were able to send down 94 overs on Monday as they desperately pushed for a win.
Dean Elgar (13) was bowled by Perera prior to the first stoppage, while Quinton De Kock made 37 before being held at backward short-leg off Herath.
Amla received able support from AB de Villiers (12) in a fifth-wicket partnership that lasted almost 25 overs but added only 25 runs.
However, after De Villiers had been cleaned up by Herath, Amla and Faf du Plessis (10) fell in quick succession, leaving South Africa struggling on 110-6.
A second stoppage aided Amla's side and JP Duminy (3) battled for 65 balls to further stem Sri Lanka's momentum.
Although Duminy and Dale Steyn were eventually dismissed, Philander and Tahir held firm to leave the hosts frustrated.