The two men, aged 20 and 21, who were with an 18-year-old man who was also arrested, allegedly broke into the enclosure in a prank while on the way back from a night out.
The men allegedly swam with dolphins before they took a seven-year-old fairy penguin, named Dirk, back to their hotel.
The men, who will appear in court on May 2, have been charged with trespassing, stealing and unlawfully keeping a protected animal, under the Nature Conservation Act.
Rhys Jones, one of the men involved, apologised on Australian TV: “Still a bit fuzzy about the whole thing but on behalf of the three of us we are very sorry and it was just a prank which went way too far.
“We are all three of us sorry to Sea World for the time lost in them searching for Dirk and we’re glad he’s all right.”
The three friends sent footage of the penguin to the TV station, to convince them that they meant the animal no harm in what they say was a prank that went too far.
Dirk was recovered when police received two calls from members of the public who saw the penguin at South Pier on Sunday evening being chased by a dog.
Sea World in Southport on the Gold Coast, said Dirk, who has never lived in the wild, was exhausted after being recovered from water near the park.
He was picked up at around 7.45pm and has now been reunited with his girlfriend, Peaches.
Sea World spokesman Renee Soutar said: “The seven-year-old bird wouldn’t have lasted long in the wild.”