Pitt later married his Mr & Mrs Smith co-star Angelina Jolie amid speculation he had left Aniston for Jolie.
Aniston clarified that the difficult times she was referring to weren't related to career opportunities after the end of Friends – which she described as "nothing but blessed" – but her personal life.
"It was more personal stuff, I had expectations about that sort of shapeshifted, so to speak. That was what was jarring, that we all had an idea of what the future was going to be and we were going to go hunker down and focus on this or that and then it all just changed overnight, and that was it.
"But again, everything's a blessing if you're able to look at life's ups and downs in that way. And if it hadn't all happened, I would not be sitting here the woman that I am today."
She also said she had resolved to pour herself into a creative outlet instead of wallowing at home.
"It just happened to be with a movie called The Break-Up," she joked, referring to the film starring her and Vince Vaughn as a couple going through separation.
Aniston's popularity due to her 10-year run on Friends, as well as a successful film career that includes Cake, Marley & Me and Horrible Bosses, has made her one of the most high-profile actors of her generation, and that fame was only intensified by her marriage to, and divorce from, Pitt.
That has meant a lot of media attention on her private life.
"I used to take it all very personally – the pregnancy rumours and the whole, 'Oh she chose career over kids,' assumption," she told THR.
"It's like, 'you have no clue what's going on with me personally, medically, why I can't … can I have kids?'
"They don't know anything, and it was really hurtful and just nasty."