Chasing a daunting 395, the Proteas were bowled out for 191 on the fifth and final day in Visakhapatnam to trail the three-match series 0-1.
But South Africa did put up a fight in their first innings, posting 431 in response to India's mammoth 502 for seven declared.
Opening batsman Dean Elgar hit 160 to boost the spirit of a side looking to rebuild after the recent retirements of greats including Hashim Amla and Dale Steyn.
"(In) Test cricket generally, experience counts for a lot. Experience is gained by playing at the highest level for a period of time," du Plessis told reporters.
"In this new phase of a lot of guys coming in, you got to give it some time."
He added: "Hash (Hashim Amla) finishing, AB (de Villiers) finishing in a year's time, we got two players with a lot of runs behind their names finishing.
"It is going to take some time to fill those shoes but we as leadership understand that it is important to be patient with the guys because they will come through again."
Elgar put together two crucial century partnerships with du Plessis, who made 55, and Quinton de Kock (111) to stand up to the Indian spinners who are formidable in home conditions.
Du Plessis said he was confident his batsmen would adapt to the turning tracks in the upcoming matches.
"Look, I think we have got a lot of confidence in our dressing room and belief because of what happened in the first innings," said du Plessis.
"I do think the pitches will probably take a bit more spin in the next two Test matches. But Dean scored a great 160 in the first innings and Quinny as well, a great combination of attack and defence."
Du Plessis also praised South Africa's leading spinner Keshav Maharaj for his three wickets in India's first innings.
"Keshav is a very, very good spinner," he said.
"He probably wasn't at his best in the second innings but I have a lot of confidence that on wickets that offer a little bit more spin, he is just as good as any one of the spinners in the Indian team."
The action shifts to Pune for the second Test starting October 10.