South Africa completed a come-from-behind 2-1 series victory on Saturday with a five-wicket win despite rain causing a delay of three hours 45 minutes before they reached their target of 211.
Chappell said India's batting had been disappointing.
He singled out the second innings collapse to 169 all out but also said the team had failed to capitalise fully on winning the toss when they made 414 in the first innings.
The Australian said some hard choices would have to be made.
"Looking at the tour as a whole there are more questions than answers," he said.
"In the next week or so when we get to India and have a chance to digest what happened and discuss it, we'll have to make some decisions about which way to go in the future. There will be some guys under pressure without a doubt."
Asked by an Indian journalist whether he thought a key aspect of the turnaround in the series had been that South Africa's senior players performed better than India's, he said: "It's hard to escape that there are things that will have to be discussed.
"The positive side is that some of the young boys performed very well. They showed guts and skill and good temperament for international cricket."
Chappell also said the pitch had not deteriorated as much as expected.
"It offered some targets for the spin bowlers but it really wasn't a minefield," he said.
"The major landing areas of the wicket were pretty good which made our batting effort on Friday that much more disappointing."
Despite the defeat, Chappell had praise for former captain Sourav Ganguly.
"He's done what he was chosen to do, which is to get in there and get runs. His performance on Friday in difficult circumstances, having to be rushed in at the last minute, was exceptional. He's done a good job."
South African captain Graeme Smith, who was named Man of the Match after scoring 94 and 55, said the win was a massive event for all the players in his side.
"To come back from 1-0 down in a three-Test series, realistically we knew how difficult it would be and I think we played superb cricket throughout. We never gave up and we showed character at key moments."
He said the series-levelling win in Durban was a breakthrough but rated the Newlands triumph higher.
"To win at Newlands, considering the conditions and that they were 260 for three at the end of day one, the way we stuck to our game plans and our beliefs and the way we worked in the field and with the bat, was incredible."
Smith and man of the series Shaun Pollock set South Africa on the way to their win with aggressive batting early in the day before rain interrupted the chase.
Left-arm opening bowler Zaheer Khan struck twice when played resumed, dismissing both Smith and Pollock, but Jacques Kallis and Ashwell Prince crafted a 77-run partnership to consign India to their third series defeat in as many tours of South Africa.