The 28-year-old midfielder was the subject of several bids from Palace, but the Premier League outfit continually failed to meet Victory's valuation of the Australia international.
Milligan, who was announced as Victory's captain on Tuesday, admitted that a move to the English top flight would have been a "dream", but insisted that he is content to remain with the A-League outfit.
"I don't think disappointment is the correct word for it," Milligan said.
"Throughout the negotiations, it was made clear from a very young age obviously I've wanted to go to the Premier League and play but we were all very open with each other and a lot of discussions took place on it.
"At no stage did I want the club to short change themselves as well. I'm very happy here in Melbourne, I wanted to make sure the club was doing things for their reasons as well.
"I didn't want to put any added pressure on the situation, but as I said, it has been clear for a long time and for a lot of footballers that that was a dream.
"The final decision was with Melbourne and the outcome is what the outcome is. I've made it very publicly known that I'm very happy here and my family is very happy here."
Victory coach Ange Postecoglou is sure that there will be more Premier League interest in Milligan in the future.
"I think it's not the last time we'll hear from a Premier League club about Mark, for sure," Postecoglou said.
"If he has the season that I believe he can and takes his game to another level, there is every likelihood that he won't be around longer too.
"Part of giving him the captaincy is to try and take him to the next level and if he does then that's great. We'll take great pride in that."
