During the third over of England's run-chase of 178, Steyn got the wicket of Jos Buttler and in the process surpassed former leg-spinner Imran Tahir's tally of 61.
Chasing 178, England fell short by just one run as they could manage 176/9 in their stipulated quota of 20 overs at the Buffalo Park on Wednesday evening.
England was cruising at 232-4 in pursuit of South Africa's 256-7 at the Wanderers when Joe Denly's dismissal for 66 sparked the late collapse.
Steyn has had constant run-ins with injuries over the last few years, especially after a career-threatening shoulder injury during South Africa's tour of Australia in November 2016.
Only 11 overs and two balls could be bowled, sandwiched between lengthy periods in the dressing room for both sets of players.
Chasing 259, the Proteas rode on brilliant innings from Quinton de Kock (107) and Temba Bavuma (98) who enjoyed a 173-run second-wicket stand at the Newlands.
According to an ICC statement, all three players have passed their fitness tests at the CSA's strength and conditioning camp.
While admitting that the Proteas were outplayed in all the three departments by the Joe Root-led side, du Plessis felt his team lacked the most in terms of batting.
Philander, 34, has played 97 matches across all three formats, taking a total of 261 wickets since his debut in 2011, before this game.
After keeping Keshav Maharaj out of their lineup for the game, South Africa did not bowl and single over of spin, which left them three overs short of their target after time allowances were taken into consideration post the match.
England won the fourth and final Test of the series by 191 runs to not just clinch a 3-1 series, but also script their best-ever result in the land since World War 1; while South Africa plunged to their new low at home.
South Africa was all out for 274 in its second innings on the fourth day at the Wanderers, way off its world-record target of 466.
All expectations are that, with South Africa facing a world-record chase, England will clinch victory and confirm a convincing 3-1 series triumph.
De Kock bagged four catches in the second innings against Joe Root's side, completing the dismissals of Zak Crawley, Ollie Pope, Jos Buttler, Chris Woakes.
Philander received the penalty for his celebration after dismissing England's Jos Buttler on the second day of the ongoing fourth Test between the two sides at the Wanderers
England made 400 all out batting first in the series decider, capped by a big-hitting 82-run last-wicket stand by Stuart Broad and Mark Wood that appeared to completely deflate South Africa.
Ben Stokes has been fined 15 per cent of his match fees and has been handed one demerit point following his verbal altercation with a spectator at the Wanderers
After Ben Stokes was dismissed by right-arm pacer Anrich Nortje on Friday, the all-rounder was heard aiming expletives at a fan.
England have become the first team to surpass half-a-million runs in Test cricket.
Ben Stokes could land in serious trouble with the match referee after he was spotted having an angry exchange of words with a spectator on day 1 of the fourth and final Test match
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