The model and presenter was dropped from the ITV1 programme just six days after being hired.
Speaking to The Mirror, Cowell described the 29-year-old as a "tough little cookie" and said: "I have spoken to Kelly on the phone and apologised.
"She was very pragmatic and very professional about it, although obviously a bit sad about no longer being a judge."
The music mogul added that he had created a new position for Brook on the spinoff programme, Britain's Got More Talent.
"I’ve offered Kelly a part on my ITV2 show. I actually liked her - she was good, she was fine," he said. "The problem was not her. Britain’s Got Talent just doesn’t work with four people.
"She is a warm person, who looks great and is very enthusiastic and that is why I spoke to her about the ITV2 show. I hope she’ll accept."
The new series of Britain's Got Talent will air on ITV1 in May.