Villas-Boas was dismissed as the Blues manager in March and Di Matteo, then serving as his assistant, was appointed as the caretaker.
"In my heart, I did think I was going to be sacked, yes," The Mirror quotes the 42-year-old as saying.
"Quite frankly, I thought it was going to happen. I more or less thought I was going to be told to leave.
"It's never nice to hear those words, although it makes you stronger for the future and it was a very emotional day for us even before I was told what they wanted me to do."
Di Matteo led Chelsea to the FA Cup and the Champions League triumph last season and was given a permanent contract before the start of the 2012-13 campaign.