Maharaj finished with figures of 5-76 as South Africa took 70 minutes to dismiss Sri Lanka for 238 on Monday.
The game had been set up for a thrilling finale as both teams required a win to keep them in contention for a place in next June's World Test Championship final.
Sri Lanka resumed on 5-205 needing 143 for victory and the home side required five wickets.
But it proved an anticlimax as the hosts ran through the batting line-up to add to their 233-run victory in the first Test in Durban.
It took South Africa seven overs to make a breakthrough on Monday, ending a 97-run partnership for the sixth wicket with Kusal Mendes caught by Aiden Markram off Maharaj.
Markram's catch was a sharp one and was only given out after a check by the television umpire to see whether it was cleanly taken.
Mendes made 46 and was followed soon after by captain Dhananajaya de Silva, who got a healthy edge to a quick delivery from Kagiso Rabada to depart for 50.
That left the tail exposed and South Africa wasted no time with Maharaj grabbing the wickets of Prabath Jayasuriya, caught at extra cover by Temba Bavuma, and Vishwa Fernando, who slogged it high to be caught by Marco Jansen.
Jansen took the last wicket of Lahiru Kumara to ensure South Africa moved to the top of the WTC standings.
