Hamilton fell to the third spot following Red Bull's Max Verstappen, who finished second after starting in 18th place, on Sunday.
The 33-year-old Hamilton, who was forced to wait for a fifth world title, congratulated Kimi. He said, "Well first big congratulations to Kimi, he did a great job today, no mistakes and he had a great start."
Hamilton also praised Dutch driver Verstappen, "Also Verstappen did a great job as well I mean he was on a slightly better tire than us at the end so it's naturally a bit of a struggle."
"I naturally thought we would've been out to do better but this was the best we were able to do in the end," he concluded.
Ferrari's Sebastian Vettel, Hamilton's only title rival, spun down to 15th on the opening lap but fought back to finish fourth - a result that means the championship remains open until Mexico next weekend.
Hamilton, the defending World Drivers' Champion and the current championship leader, now has a 70-point lead over his four-times champion rival with 75 points remaining to be won from the last three races.
Kimi's victory was very special for him as he will leave Ferrari at the end of 2018 and will return to Sauber.
This was his first win since the Australian Grand Prix of March 2013, a gap of 113 races dating back to when he was racing for Lotus, and 21st of his career.