Overnight unbeaten on 26, the left-hander was expected to resume his innings along with the other not out batsman Cheteshwar Pujara but at the last minute decided not to do so because of a blow he had received at the nets before the play started.
He came to bat when when six wickets were down and did not appear to be in any discomfort before eventually top-scoring with 81.
Dhoni said Virat Kohli got less than 10 minutes to prepare himself before going out there in the middle in place of Dhawan.
"It was quite late and we could only give maybe 5-10 minutes' notice to Virat that he would go in to bat. That's one area which we could have handled a bit better but it's something that we will have to take it in our stride.
"We went to practice and the wicket wasn't good for it. A few of the batsmen batted and Shikhar got hit and left. After that, I had padded up and I went in. He (Shikhar) was a bit uncomfortable but he didn't react and say that he can't bat," Dhoni said.
"Shikhar came back to the dressing room and Duncan and I were there. By that time, I had finished my batting and I found the wicket to be a bit uneven. But by the time we came back, it was quite close to the start of play. And there, we realised that Shikhar wasn't really 100 per cent fit to go into bat.
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