The Proteas still trail by 154 runs after being asked to follow on as they were all out for 275 at the end of Day 3, replying to India's mammoth 601/5d in the first innings.
Maharaj, who top-scored for the tourists with a dogged 72 in the first dig, remained unbeaten on 3 from 20 balls while Philander raced to 18 from 20 deliveries, hitting two sixes.
The pair added an unbroken stand of 43 for the eight wicket after South Africa were reduced to 129/7 post lunch.
Familiar tormentors Ravichandran Ashwin (2/45) and Ravindra Jadeja (2/47) spun a web around the more accomplished South Africa batters as none except Temba Bavuma (38) to a certain extent could score runs.
Quinton de Kock (5) was the first to depart after the first session, trying to slog-sweep Jadeja and losing his stumps in the process.
Ajinkya Rahane then pulled off a stunning catch to remove Bavuma off Jadeja while Senuran Muthusamy (9) was removed by Mohammed Shami, Rohit Sharma taking a catch at second slip.
Earlier, Ashwin took two wickets as India reduced South Africa to 74/4 at lunch.
The session though belonged to India stumper Wriddhiman Saha's brilliance behind the stumps as the 34-year old took a stunning one-handed diving catch off Umesh Yadav's delivery to dismiss Theunis De Bruyn (8) in the sixth over of the innings.
Saha's effort left all his teammates amused as skipper Virat Kohli came running to congratulate the dimunitive wicketkeeper whom he hailed as the best in the world few days back.
Saha had taken a similar catch to remove the same batsman in the first essay, flying to his right to grab the ball with both hands right in front of first slip off Umesh's bowling to dismiss de Bruyn as the tourists slumped to 53/5 on Day 3.
The Proteas were eventually bowled out for 275, still 326 runs behind India's mammoth first innings score of 601/5d.
The script did not change in their second dig as Ishant Sharma first trapped Aiden Markram (0)) in front, de Bruyn was next to go as skipper Faf du Plessis promoted himself up the order and came out to bat at No.4.
Along with opener Dean Elgar, the pair added 49 runs for the third wicket before du Plessis' time at the crease came to an end as Ashwin had him caught behind with Saha taking the catch on his third attempt.
Du Plessis took 54 balls to get to 5 but his grind was done as Elgar continued to fight on at the other end. Mohammed Shami bowled probing lines but Elgar managed to reach 48 from 72 balls with the help of eight fours before holing out to Umesh at mid-off Ashwin.
On Day 2, Ashwin had snared four wickets to dismantle South Africa with the assistance Umesh (3/37) and Shami (2/44). Keshav Maharaj hit a career-best 72 but that was not enough as the tourists were all out for 275.
Brief scores: 1st innings: India 601/5d; South Africa 275; 2nd innings: 172/7 (Dean Elgar 48, Temba Bavuma 38; R Ashwin 2/45, Ravindra Jadeja 2/47)
( With inputs from IANS )
