"It's been hard work. The first two Tests of this series have been really tough," said Paine who took over from Steve Smith after he was suspended following the plot to cheat South Africa during the third Test at Newlands in Cape Town.
"We've got some inexperienced players in terms of Test matches played and to get a win like that against the best Test team in the world is going to give them a huge boost of confidence. I'm relieved personally."
Set 287 to win, India resumed the final day in Perth on 115 for five. But there was no fight in the tail allowing the hosts to record their first success in seven Tests spanning almost 10 months.
Kohli, who was involved in arguments with Paine on the pitch, was munificent in defeat. "We had the belief we could do it," he said. "But they were more relentless and got the balls in the right areas for long enough."
The third match in the four Test series starts in Melbourne on 26 December.