It was the seventh century in the 22-year-old's ODI career and included 10 fours and three sixes.
Two days after winning the first ODI by six wickets, Afghanistan made a bright start as the openers capitalised on winning the toss.
Gurbaz and Riaz Hassan added 88 for the first wicket before Aiden Markram had Hassan leg before for 29.
That brought in Rahmat Shah (50) who shared a 101-run partnership with Gurbaz before the opener fell shortly after reaching his milestone, bowled by Nandre Burger for 105.
The innings slowed with that dismissal although Azmatullah Omarzai hit the accelerator with a rapid, undefeated 50-ball 86 which included six sixes, to ensure an awkward chase for the Proteas.
