Top seed Murray had to come from a set down to beat the defending champion 5-7 7-5 6-3 to claim the trophy in the traditional Wimbledon warm-up event.
After taking the difficult decision to sit out the French Open earlier in the month, world number two Murray had not played a competitive match for some time and he was pleased to come back strong, with victories over Cilic, Jo-Wifried Tsonga and Nicolas Mahut over the course of the tournament.
"I played two top grass-court players the last couple of days and they were tricky matches," he said.
"Mahut is also a very good grass-court player. That was a tough start for me and, with the rain delays and stopping and starting, it's been a long week, a lot of long days.
"I'm happy I managed to finish it with a win. Obviously before the start of any week you sign up for a win but having not played for a while, it's more difficult."
Murray raced into a 4-1 lead in the opening set before several unforced errors and a troublesome-looking fall saw Cilic claw his way back into the match.
The Croatian claimed the first set, with Murray admitting he had struggled but believing his game is heading in the right direction.
"I just made some bad mistakes when I was up in the first set, like I had done in quite a few of the matches this week," he conceded.
"But I kept trying to go for it. I was trying to take chances, and I felt like I was dictating a lot of the points.
"I created loads of chances today [Sunday], a lot of chances. I think with a few more matches and a few more days' practice, I think I'll do a better job converting them and won't have the little slip-ups I had this week."
The first-set slip seemed to leave Murray in quite substantial pain, with the Brit's scream of agony audible throughout centre court, and he revealed afterwards he was suffering discomfort in his groin.
"It hurts," he added. "You never know until you start moving around on it how it feels. When you sort of do the splits and you're not in control, it hurts the hips a little bit.
"But after a game or two I knew it was fine, but you still become a little more cautious with your movement for a few games, and maybe it contributed to the way I finished the first set."
Cilic, who has only beaten Murray once in their previous nine matches, felt he played well early on in the match but he felt he struggled to keep the same effort going throughout.
"I would say the match was on an extremely high level," said the world number 12.
"Maybe just towards the end of the match, after two or two and a half hours of play, it is not easy to keep that level of play, but definitely those first two sets was great, great tennis.
"I was playing well and I was very positive on the court, which I like the most."
Murray followed the final by playing in a pro-celebrity match in aid of the Royal Marsden Cancer Charity, and it was later confirmed he had donated his £73,000 prize money from the tournament proper to the cause.
A Twitter post from the LTA read: "We're delighted to confirm @andy_murray has indeed donated his #aegonchampionships prize money (E86300) to #RallyAgainstCancer @RoyalMarsden"
The Royal Marsden Centre has been treating Murray's close friend, Davis Cup doubles player Ross Hutchins, as he battles Hodgkin's lymphoma.
The Rally Against Cancer match saw Murray and Tim Henman take on Czech pair Tomas Berdych and Murray's coach Ivan Lendl. There were also appearances from London mayor Boris Johnson, Virgin supremo Sir Richard Branson, actor Eddie Redmayne and comedians Michael McIntyre, Jimmy Carr and Jonathan Ross.