Kaizer Chiefs' Nkosingiphile Ngcobo and Orlando Pirates striker Zakhele Lepasa were handed starts along with Mamelodi Sundowns' Promise Mkhuma started.
It was Mkhuma who had the chance to put South Africa in front earlier on, but a defensive clearance put him off with Lepasa failing to pounce on a ball from Ngcobo earlier on.
The breakthrough arrived in the last four minutes of the first half when Lepasa met a cross from Fagrie Lakay to send in a sweet finish from the far side of the area.
Saudi Arabia pulled level with the last kick of the half through a smart finish from Ayman Alkhulaif after the visitors went to sleep.
The Saudis got a chance to go ahead from the penalty spot minutes after halftime, but goalkeeper Sifiso Mlungwana showed up and denied Khalifa Aldawsari.
David Notoane went to the substitutes' bench on 54 minutes and introduced Goodman Mosele who came on for SuperSport United midfielder Jamie Webber.
Katlego Mohamme should've restored South Africa's lead midway in the second half with a header from a corner-kick by Lakay, but went inches wide.
Instead, Saudi Arabia turned the match around three minutes from time when Nasser Oloran converted from the spot after a poor challenge by Given Msimango.
Notoane's side drew level within a minute after Lakay carved an opening on the near side of the area to finish from a tight angle.
The Saudis had the final say in stoppage time when Ramzi Holan charged into the six-yard area to fire in the winner.