With the ball disappearing to all parts of the ground, it required a run-out to finish the job, Sam Curran throwing down the stumps as Maharaj sprinted to bring up the century stand.
Captain Joe Root paid tribute to the performances of Ollie Pope, who made 135 not out, and Dom Bess, who took five wickets in the first South African innings.
“It’s a great template for how we want to play our cricket moving forward, big first-innings score and drive the game from there,” he said at the presentation.
“I think Ollie batted beautifully with (Ben Stokes) – a brilliant partnership that put us in a commanding position.
“Then the way Bessy bowled was fantastic in that first innings. From that point on, we always felt we were in control of things.
“Throughout this series, we’ve had four guys under 25 making five-fors or hundreds, which is a great place to be.
“That’s something that we want to keep continuing to provide – an environment where that becomes possible and keep giving those guys confidence.”
Discussing his batting, which included a 203-run partnership with Stokes, man of the match Pope said it was an amazing feeling.
“But it wouldn’t have counted for much if we hadn’t won the game, so that’s the most important thing. To get over the line is an even better feeling.
“To bat with Stokesy is a privilege. He just keeps getting better and better.
“To see how he goes about building his innings and the tempo he plays at is awesome to watch. I was in a pretty good seat to watch another special innings from him.”
South Africa won the first Test in Pretoria by 107 runs but the tourists bounced back with a 187-run win in Cape Town.
The result marks a notable achievement for Root and his side, the first time England have enforced a follow-on overseas since 2013 and the first occasion they have done so successfully since 1992 in Christchurch.
The fourth and final Test starts on Friday in Johannesburg.