Maharaj finished the match with figures of 9-97 to win his second player of the match award in the series and also won the player of the series award with 16 wickets from two Tests.
Only three Bangladeshi batsmen got into double figures in the second innings with Liton Das being the top-scorer with 27 runs.
Bangladesh resumed the day’s play on 27-3, chasing a mammoth 413-run target.
The Tiger’s hope of delaying the inevitable was crushed inside the first five overs of the day when Maharaj dismissed Mushfiqur Rahim and Mominul Haque for one and five respectively. Harmer handed Yasir Ali a duck to reduce the tourists to 44-6.
Liton and Mehidy Hasan Miraz (20) then entertained the small number of Bangladesh supporters in the stands with some boundaries before falling victim to the left-arm spinner Maharaj.
Taijul Islam and Khaled Ahmed departed without troubling the scorers as Bangladesh got bundled out for a two-digit score for the second time in the series.
Earlier, South Africa rode on fifties from Keshav Maharaj (84), skipper Dean Elgar (70), Temba Bavuma (67) and Keegan Peterson (64) to post 453 in the first innings after opting to bat first. Taijul Islam claimed a six-wicket haul for Bangladesh.
In reply, Bangladesh folded for just 217 in their first innings, conceding a 236-run deficit. The hosts chose not to enforce follow on. They batted for 39.5 overs and declared their second innings on 176-6 to set an improbable target for the Tigers.
Bangladesh batted just 9.1 overs on Day 3, where they lost three wickets with hardly any runs on the board. The South African spinners finished what they started in the next morning.
With the defeat, Bangladesh has lost the series 0-2. They earlier lost the first Test by 220 runs.
This is also Bangladesh’s eighth Test defeat in the same number of games in South Africa and also the fourth time they have been clean-swept in an away Test series against South Africa.
This Test also concluded Bangladesh’s tour to South Africa, which had started promisingly with their first ever One-Day International victory against the Proteas in South Africa. The visitors lost the following ODI but then made history by winning the third ODI to clinch their maiden ODI series win in South Africa.