The 21-time Grand Slam champion called an early end to her season after the US Open, where her semifinal loss to Italy's Roberta Vinci ruined her hopes of completing the calendar year Grand Slam.
"It's the same as Rafa," Mouratoglou said. "It's just playing for so many years, the cartilage is [almost] gone. Not all of it, but a big part, so the bones just hit themselves.
"She has bone bruises, and if you keep on playing with this for too long, too much, the next step is a stress fracture."
Williams returned to training this week after almost two months off and Mouratoglou said they had always planned a break to allow the injuries to heal.
"There was no other option, and we knew that at some point we had to do it, because she plays with pain all the time," Mouratoglou said. "The injury can get really worse, and at her age her career could really be in danger if she went too far and got more injured, like Rafa did in the past.
"He kept on playing with the same problem and then it got worse and he had to stop for almost a year, we don't want this to happen. She is 34, if she has to stop for a year then it is really bad for her future.
"I'm not a doctor, she has treatment, but I know without rest there is no chance because you keep on hitting the bones all the time."
Mouratoglou said the loss in New York was due to a combination of injury and stress.
"First, she had pain this day," he said. "With the knees you never know, sometimes the pain is much more [than other days]. That was the first thing she said when she came to the [practice] court: 'My knees hurt so much today.' So she was really struggling to move.
"I think also the tension went to another level, which I expected, because the closer you get to a final goal, obviously the stress goes to another level. I take responsibility on that because I couldn't find a way to make her handle it better. I think she did incredibly well the whole tournament because she found a way, especially the match against Venus [Williams], because Venus pushed her to play really her best and the level of the match was amazing.
"So I was impressed by the way she was handling it and maybe that's one of the reasons I thought it would be OK. So a bit of both factors, she was not able to play her level and then you know what happened."
Mouratoglou said missing out on the calendar Grand Slam left Williams incredibly down.
"She was depressed," he said. "The reaction was quite strong. "She was really, really affected, which I think is normal when you are Serena.
"She does everything with 100 percent of her heart so you are more disappointed when you don't reach your goal. Plus, she she has a level of expectation that is much higher than anyone."
The Frenchman, who has helped Williams to eight grand slams in 14 attempts since becoming her coach in June 2012, said he did not speak to her for more than two weeks after the US Open.
"She doesn't want to talk when she's depressed," he said. "But it's better. Because I represent tennis, and when you are [recovering] after something like this, you have to see people who don't represent tennis.
"You have to change your mind. Otherwise you keep on thinking about it. I didn't force it. I know her and I understand also that she needs a break. It's fine.
"I think it's good if she just pushes herself and she sees people and she goes out a little bit. It helps you also to think about something else. You have to erase that from your memory."
Mouratoglou said he was not worried about the possibility of any delayed reaction from Williams and said she was raring to go for 2016.
"She came back to practice this week and she's already so excited to play, which is good, but the preseason is long so you have to manage your motivation," he said.
"If you go too fast then the last weeks before the tournaments, you're going to go down, and that's the moment when you need to go up, so you have to manage it. I'm happy to feel her so excited. I told her to calm down."