The 19-year-old, a member of the Toyota CSA Academy team, finished 34 seconds ahead of South African elite road race champion Darren Lill (Bonitas) in the six-stage race.
Dennis van Niekerk of MTN Qhubeka, who won the final stage, was a further 24 seconds behind in third.
"I went into the race with the intention of having a good result, but knew that winning would be a huge task in the circumstances," Meintjies said.
"I'm obviously very happy with my result, but grateful to my team for their amazing support both on and off the bike."
His team said in a statement that Meintjes would next focus on the inaugural Tour de Free State later this month and the Under-23 World Road Championships in Norway in September.