A man wearing a Croatia soccer jersey walked onto the court just after the players finished their match and approached Croat Cilic as he was preparing to shake the chair umpire's hand.
After shaking Cilic's hand, the man was intercepted and escorted off court.
Cilic later played down the incident, but the embarrassing security breach has thrown the spotlight on security at the Australian Grand Slam.
The man, 22, from Melbourne, would be "charged on summons with disrupting proceedings and unauthorized entry to an arena," a police spokesman said in a statement on Friday.
Tournament organizers would not provide immediate comment.
Players still remain vulnerable to crowd invasions despite pledges by tournament organizers to bolster security after Monica Seles was stabbed in the back by a Steffi Graf fan at a Hamburg tournament in 1993.
A man was charged after he invaded the court at Arthur Ashe Stadium at the U.S. Open last year to kiss Rafael Nadal on the cheek.
Roger Federer was unnerved when a spectator jumped from the stands and tried to put a hat on his head during the final of the French Open.