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Van Zyl crossed the finish line in 32 minutes, 20 seconds, to improve her previous career record of 32:50 set in Durban in June 2011.
Her time equalled Zola Budd's personal best as the third fastest 10km performances by South African women on the road.
Budd clocked 32:20 in Bloemfontein in August 1983, at the age of 17, which still stands as the SA junior record.
Only former half-marathon world record holder Elana Meyer and Colleen de Reuck, who is now a US citizen, have run faster over the distance.
Van Zyl's training partner and fellow Olympian, Rene Kalmer, took second place in 33:33.
Meanwhile, at the Johannesburg leg of the women's 10km series, held on the same day as the Western Cape race as part of Women's Day celebrations, Lebogang Phalula strode to a decisive win in 36:01.
Phalula was more than a minute clear of Mapaseka Makhanya, who finished second in 37:09.
