The actor and singer played Joker in the 2016 movie, opposite Margot's Harley Quinn, and during the press tour for the blockbuster, they both sold the media on the prank story.
Five years later, Leto has come clean, insisting he only gave her a vegan cinnamon bun.
In an interview with GQ about his various movie roles, Jared said, "It's funny how all this stuff takes on a life of its own. I never gave Margot Robbie a dead rat, that's not true. I actually gave her a lot of... I found this place in Toronto that had a great vegan cinnamon bun... so that was a very common thing."
Margot opened up about rat-gate in an interview just before the film's big release and claimed the rodent she was sent was alive.
"(I got a) nice love letter with a black box with a rat in it - a live rat," she said. "If Harley got something from Joker, she'd probably cherish it."
The 30-year-old actress embellished the rat tale, admitting she was scared of the creature at first but kept it and grew quite fond of her pet, until she had to give it up.
"I was like, 'I'm not going to kill him'," she explained. "So I ended up keeping him as a pet. I ended up getting him, like, a sweet little play pen, a slide, a hammock, and a leash because I wanted to take him to set and walk him around... But then our landlord at the place I was staying found out."
Meanwhile, Leto, who has reprised his Joker character for Zack Snyder's upcoming "Justice League" epic, reveals he loved stepping into the villain's shoes again.
"I guess it's this generation's version of taking on an infamous Shakespearean character," he tells GQ. "Lots of people have played the part before, lots of people will play it in the future, so really it's an opportunity to do something new and to explore challenging territory."
Leto shot new scenes for Snyder's four-hour blockbuster and appears at the end of a new trailer, chatting to his superhero nemesis Batman, played by Ben Affleck.