Morkel twisted his ankle in the first session of the day and is now out of this Test match, as well as a serious doubt for the second Test in Durban.
"Losing Morne was very painful. From then, we knew that Dale Steyn, Jacques Kallis and I will have to share the bowling load, with the spinners going for runs. It was a tough day to be in Graeme Smith's shoes, one of those days," said Philander.
"He won't be bowling further in this match," Philander confirmed.
Cheteshwar Pujara's sixth Test hundred and a 191-run partnership with Virat Kohli made sure that India took a 320 run lead in the match.
This was after South Africa were bowled out for 244 in reply to India's 280 in the first innings.
"The bowled better in the first innings, while pitching it in the right areas and into the stumps. We bowled a bit better in the second innings, but also the sun was shining when they came to bat. So it became a little easier to bat as well. It was a little overcast when we batted so it helped the Indians as well," Philander tried to put up a brave front.
Philander is perhaps the only member of their team who could hold his head up, with a 50 in the first innings to go with his 100th Test wicket in the second innings, scalping Shikhar Dhawan.
"I take pride in my batting and work hard at it in the nets as well as when I am away from the national team. I like batting under pressure and making a play for the team when the situation demands. I was reminded about the 100th wicket quite a bit. I prepare for every game the same way and hopefully can take a few more wickets for South Africa."