Compensation is determined on the player's age and contract offer, which has resulted in the round two pick.
The Swans will be able to use it after their original second-round selection, or they can trade it.
Malceski told Swans coach John Longmire on Monday afternoon he wanted to move to the Suns, where he will take on a leadership role and will also reportedly join the club's academy as a development coach.
The Swans were disappointed to lose him but understood his decision.
"We would have liked to have seen Nick finish his career with the Swans and I'm sure he would have too," football manager Dean Moore said.
"We put a really good offer to Nick but unfortunately he's been offered a deal too good to refuse.
"While obviously disappointed to lose someone of Nick's calibre, who arguably had his best season this year finishing with All Australian selection, we understand his reasons for accepting the Suns’ offer.
"We thank Nick for his contribution to the club and he will always be remembered for his outstanding 2012 Grand Final and the role he played at the club over the past 12 seasons."
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