With Nathan Coe not offered a new deal by Victory, Vukovic appears set to be Kevin Muscat's first choice next season - with Lawrence Thomas waiting in the wings despits his solid finish to the campaign last season in which Melbourne won the double.
Vukovic and his wife Kristy are expecting their first child in July, with the 30-year-old declaring that move closer to family on the east coast was a key factor in his decision to leave Glory.
"The best interests of our child will always come first and while I leave Perth with a heavy heart, the opportunity to move closer to home was very important to Kristy and I," Vukovic said.
"Melbourne Victory is the biggest club in the country and I look forward to working with Kevin and the team as the club looks to build on last season's success.
"I have always admired Melbourne Victory from afar and I can't wait to play in front of packed stadiums week in, week out."
Vukovic has made 227 A-League appearances – just one short of games record holder John Hutchinson – during his time at Central Coast Mariners, Wellington Phoenix and Perth Glory.
"Danny is the most experienced goalkeeper in Hyundai A-League history and we are delighted to secure his services for the next three years," Melbourne Victory coach Kevin Muscat said.
"He has proven himself as a quality goalkeeper time and time again over the past 10 years and having played and coached against him, I have always been impressed with him as a person and by his attitude and desire to succeed."
