Australia were bowled out for just 131 on the fourth morning in Hyderabad to lose by an innings and 135 runs and go 2-0 down in the four-match series.
"I think India deserve a lot of credit, they outplayed us in all facets of the game in this Test match," Clarke said.
After declaring their first innings on 237 for nine on day one, Australia then saw hosts India run up a mammoth 503 in reply with Murali Vijay (167) and Cheteshwar Pujara (204) putting on 370 for the second wicket.
"I thought the partnership the two Indian players put on in the first innings was fantastic, and I think we need to learn from that," added Clarke, who top-scored for his side with 91 on the first day.
"I think our batters have to take responsibility. We haven't scored enough runs in our first innings in both our Test matches, and that's unacceptable in the best of batting conditions."
Australia have time to regroup with the third Test in Mohali not starting until March 14, and Clarke has promised his side will make full use of the time.
"There will certainly be no break in between, there'll be nothing but hard work. You don't get better sitting on the couch, that's for sure," he said. "There will certainly be no stone left unturned leading up to the third Test match."
India captain Mahendra Singh Dhoni was keen to share the praise around, both among his team and the coaching and backroom staff.
"I think I've got a very good side, I've always said that," he said. "I think it's a collective effort and credit goes to each and every individual."
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