Seventh seed Cilic made it through to a third final in as many weeks when he emerged victorious in a battle of big servers against American Isner in a rain-delayed semi-final that did not start until close to midnight on Saturday.
Fourth seed Anderson had no such delays in the first semi and was on and off the court in a flash after easing past a nervous American qualifier Steve Johnson 6-2 6-4 in the afternoon in south Florida.
When the second semi-final finally got underway, Cilic's first serve was almost unplayable but he could not convert any of his four break points against Isner in the first set, which went to a tiebreak on the hardcourt surface.
Isner won the first three points but Cilic stormed back to take the next five and ultimately the set.
Cilic quickly broke Isner in the second set and continued to serve strongly, closing out the contest just before 1 a.m. on Sunday.
"It's been probably the best three weeks I've played in my life," Cilic, who won in Zagreb a fortnight ago before losing in the final last week in Rotterdam, told reporters.
"With John, you have to be careful always with his big serve (but) maybe John was struggling a little bit with his neck or back. He wasn't hitting his first serve as big as usual."
Johnson, meanwhile, steamrolled his way to his first ATP semi-final, knocking off top seed Tommy Haas along the way, but his fairytale run ended against the immovable force of Anderson.
Anderson, the 2012 champion who lives in Delray Beach, broke in the first game and never looked back as he held serve easily throughout.
"Getting that break was really key for me," Anderson said.
"I've always enjoyed playing here. The surface is one I enjoy playing on."
Johnson admitted to nerves: "I was definitely a little uptight out there," said the former U.S. collegiate champion, who could make no headway against his opponent's serve and never even held a break point.
"I think if I'd won that first game it would have changed the whole course of the match. But credit to him, he played a good game and returned very well today."