West Indies require 275 runs to make South Africa bat again and with the weather set fair for the next two days, the rampant Proteas will be confident of completing the win.
Philander bowled with impeccable line and length to grab four wickets as West Indies were bowled out for 201 in their first innings, before he removed left-handed opener Devon Smith after home skipper Hashim Amla asked the visitors to follow on.
Marlon Samuels (13) and Leon Johnson (31) will resume on Saturday hoping to lead the West Indies rearguard on a pitch that remains good for batting.
The Proteas do have problems of their own though, wicketkeeper Quinton de Kock did not appear after he rolled his ankle in the warm-ups, while Faf du Plessis will return to hospital on Saturday for more tests after he was laid low by a mystery stomach ailment.
Both are in doubt for the remainder of the test.
At one stage South Africa had just seven of their starting line-up on the field when both Dale Steyn and Philander went off with muscle complaints.
Replying to South Africa's score of 552 for five declared, West Indies made a promising start to their innings in the morning session when they put on 72 for the first wicket before Smith was controversially given out caught behind by third umpire Paul Reiffel when he had 35.
The top four West Indies batsman were all out for between 30 and 35 as they failed to build on confident starts.
South Africa continued to pick up wickets at regular intervals and with fast bowler Kemar Roach not batting due to an ankle injury, West Indies were bowled out shortly after tea.
Philander was the pick of the home pacemen with four for 29, well backed up by Morne Morkel who took three for 55.
The tourists were in early trouble in their second knock when Smith was caught by substitute fielder Temba Bavuma off Philander for five as he got an inside edge onto his pads that flew to point.
And when Alviro Petersen held a fine catch at second slip to dismiss Kraigg Brathwaite (20) off Morkel as the light faded, so, it seems, have the hopes of the West Indies.
(Reporting by Nick Said; editing by Martyn Herman)
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