Lebopo won Saturday ahead of compatriots Moeketsi Mosuhli and Teboho Sello. Zimbabwe's Stephen Muzhingi overtook Lebopo's brother Warinyane in the final stages to claim fourth.
Russia's Olesya Nurgalieva won the women's event in 3:41.52, with twin sister Elena just behind in second. The sisters have not finished lower than fourth in the last seven races.
A record 21,000 runners entered the Two Oceans, which boasts a scenic but demanding route that touches both the Atlantic and Indian oceans along the hilly coastline near Cape Town.