"It was just a feeling that I knew that I cannot give my best on the court, that I cannot give my best game and my best tennis, especially at this stage of my career, at such a big match," he said.
"It was very, very difficult to deal with it. That was the only thing.
"But, otherwise, it didn't hurt so much that it was putting me in tears. It was just that feeling that I wasn't able to give the best."
But he found little sympathy from British TV personality Morgan, who posted a provocative tweet blasting the runner-up.
Morgan was lashed by other Twitter users for his insensitivity, including athletes and commentators.
But he refused to alter his stance.
Cilic was attempting to become the first Croatian to win the title - and second ever - since his one-time coach Goran Ivanisevic denied Pat Rafter in a classic five-set decider in 2001.
"It was definitely one of the unfortunate days for me to happen. I got a really bad blister," the sixth seed said.
"Even I felt it in the match with (Sam) Querrey in the semis. Fluid just came down under my callous in the foot.
"I want to thank the physios here, Alejandro and Graham and Dr Phil. They helped.
"The last 30 hours, they were just constantly almost with me. They did as much as they could, but unfortunately I still felt the pain.
"Every time I had to do a reaction fast, fast change of movement, I was unable to do that."
Despite his heartache, Cilic accepted Federer as a worthy winner of his record eighth Wimbledon men's singles crown.
"I don't want to put down his victory in any way," Cilic said. "He deserved it completely. These things are part of the sport."