Cilic dropped just one set in five matches in the 400,000-dollar event at the Nungambakkam Tennis Stadium to clinch his fourth career title in six ATP finals.
"This was the longest final I have played in and also the toughest," said the 21-year-old. "It was a mental battle out there with a lot of long rallies and returns.
"It is not easy to maintain your top game over such a long match. It makes me very proud that I have once again come out well in the first week. It was not easy to adjust to the heat.
"A lot of sweat and hard work went into winning this week. I am very pleased really, very happy."
Cilic said he will fly to Melbourne later on Sunday night to rest and practice ahead of the Australian Open. "No tournament for me, I want to be fresh for the Open," he said.
Wawrinka secured the first break of the match in the eight game, but Cilic broke back immediately in the ninth to force the set into the tie-breaker, which the Croatian won easily.
Schumacher impressed after visit to MercedesThe Swiss star, who called for the trainer in the first set for a neck strain, lost his serve in the second game of the second set, but broke back in the third to draw level.
Cilic wasted two break points for a 5-3 lead as Wawrinka fought back to take the match into a second tie-breaker, which the tall Croatian dominated once again.
"It was tough to lose such a close match because I thought I played really well," said Wawrinka, 24, who has now lost six of his seven career ATP finals.
"I threw everything I had into the match, but was unable to score the crucial points. Maybe, I need to be more aggressive during the tie-breakers."
Warwinka said he will take part in the Sydney International this week to fine-tune his game for the Australian Open.
"I have a week in Sydney to be ready for the Open, but it has also been a good week in Chennai," he said. "I am happy with my game and felt good to reach the final in the first event of the new year."