He had been out for nearly a year with a hip injury that required surgery.
With momentum back on his side, Cilic looked comfortable in the west London sunshine as he grabbed the only break in the final set to claim his first title of the year. "I'm really pleased with the way I have played throughout the whole week".
"I wouldn't say I'm a contender for a trophy or anything like that", said the 31-year-old.
But it was the double fault midway through the match which Djokovic feels cost him so dearly.
He saved a first break point at 1-1 but then needed to save five more at 3-3, and was lucky that Cilic could not execute on any of them when given the chance.
Cilic said, 'Just before the tournament in Wimbledon, I went to see the specialist for a pedicure at Wimbledon, and the lady helped me a lot.
"I felt that when I'm going to raise my level of the serving, I'm going to be the one who can even take control of the match, " Cilic said.
Cilic arrived here with a proud record on the Queen's Club grass.
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Cilic can get nervous but served it out comfortably and will fancy his chances of another deep progression at Wimbledon.
Djokovic had his moments on Sunday, forcing Cilic through 10 minutes of angst at the start of the second set, but after an hour and a half Cilic was making him earn every point.
Firing some superb returns, he converted his third set point when Cilic netted a backhand.
Videos picked up by fans show Kyrgios playing the circle game with his camp, clearly more interested in having a laugh than trying to break down Cilic's serve.
It's been a long year for Novak Djokovic.
Petra Kvitova hit back from a set down to beat Magdalena Rybarikova and retain her Nature Valley Classic title in Birmingham.
Cilic, runner-up to Roger Federer at Wimbledon last year and this year's Australian Open, was relentless, however, and seized on a couple of Kyrgios groundstroke errors in the opening tiebreak to pocket the first set. I played a lot of three-setters and a lot of tennis.