Touring South Africa completed victory inside three days after bowling West Indies out for 222 on Saturday, having set them a target of 263 to win the match.
The rain-affected first game in Trinidad was drawn but the second Test victory means South Africa have won 10 successive series against the Windies.
Maharaj, named man of the series, finished with 3-37, going past Hugh Tayfield's tally of 170 Test wickets to set a new standard for South African spin bowling.
Fast bowler Kagiso Rababa, who also took three wickets, is now on 299 Test victims.
It was a close call for the touring side in a low-scoring match as the Windies fell agonisingly short.
They begun their chase with more than two days to play, but lost opener Mikyle Louis cheaply for four as he nicked a catch to Wiaan Mulder at slip off Rabada.
Captain Kraigg Brathwaite was the next man out but not before adding 42 runs with Keacy Carty for the second wicket.
When the experienced Jason Holder fell without scoring to leave West Indies on 6-104, it looked an uphill task for the home team.
Joshua da Silva and Gudakesh Motie, however, shared the best Windies partnership of the series, adding 77 runs to reduce the target to 82, before Motie was lbw to Maharaj for a Test-best 45.
Maharaj trapped Da Silva lbw for 27 and a brilliant one- handed diving catch from skipper Temba Bavuma sent back Shamar Joseph before Maharaj had Jayden Seales was caught by close-in fielder David Bedingham.
South Africa had resumed in the morning on 5-223 with a 239-run lead but the 22-year-old Seales ran through the tail to return Test best figures of 6-61 as the last five wickets fell for 22 runs.
8°C