The triumph bettered their 4-1 victories over Namibia, Gabon and Swaziland since Bafana Bafana (The Boys) were readmitted to international football 15 years ago following three decades of isolation.
And the architects of the record win in the 200th international played by South Africa were Durban-born strikers Sibusiso Zuma, who scored twice, and substitute Siyabonga Nomvete, whose goal completed the success.
Success lifted Group 11 leaders South Africa on to ten points, five above Congo, who were playing in Zambia later Saturday. Only the winners of the four-nation group are guaranteed a place at the 16-team finals.
Nasief Morris claimed his first goal for South Africa to open the scoring 13 minutes into a match staged in chilly, overcast conditions at the Absa Stadium in the Indian Ocean city.
Any hope Chad, beaten 3-0 at home by South Africa last March, had of causing an upset virtually disappeared before the kickoff when a pay dispute deprived them of several first-choice players. And the central Africans did not threaten to score until 60 seconds from full-time, when South African goalkeeper Rowen Fernandez stretched to push away a goal-bound header.
South Africa had a penalty appeal for handball by captain Lucien Teinkor rejected, before taking a 13th minute lead when Morris stroked a spot-kick into the corner past goalkeeper Mamadou Bouba, who fouled Zuma.
Zuma displayed clinical finishing to double their advantage ten minutes later with a low volley off a Delron Buckley cross. The local hero with the peroxide blond hairstyle struck again with 33 minutes gone, after outsprinting two defenders and rounding Bouba to calmly fire home.
The South African side coached by Carlos Alberto Parreira, who led his native Brazil to the 1994 FIFA World Cup™ title, showed less urgency after half-time and seemed content to retain possession against their demoralised opponents. But in a flash of brilliance midway through the second half, Elrio van Heerden dribbled past five opponents, before crossing for Nomvete to score from close range.