Pitt ended up winning in the Best Supporting Actor category, and his co-star, Margot Robbie, took to the stage to accept the award on his behalf and to read a prepared speech.
"Brad couldn't be here tonight due to family obligations," Robbie explained to the crowd, which included British royalty Prince William and Kate Middleton.
Robbie then read Pitt's speech, which began with the Brexit joke, "Hey, Britain, heard you just became single, welcome to the club."
The Australian actress then read through the rest of the speech before ending on the A-lister's joke about the royal family.
"He says that he is going to name this Harry because he is really excited about bringing it back to the States with him," Robbie read holding up the statue, as gasps rang out in the Royal Albert Hall. "His words not mine, thanks!"
The camera then cut to royal patrons William and Kate, who appeared to be tickled by the joke, openly laughing as Robbie exited the stage.
Awks. The moment at last night’s @BAFTA Awards when Brad Pitt’s acceptance speech (read by Margot Robbie) joked about Prince Harry’s move to America 🇺🇸 Oh, how William and Kate laughed 😂 pic.twitter.com/FPV5ad9317
The quip was, of course, a response to Prince Harry and his wife, Meghan Markle's, recent exit from the British royal family. The pair announced their intention to step down as senior members of the family and shortly after, Queen Elizabeth II confirmed that they would be ending their royal duties and splitting their time between North America and the U.K. with her support.
Pitt wasn't the only star to make a Prince Harry joke. Rebel Wilson also threw out some jokes about Harry and his uncle, Prince Andrew, which received a much less enthusiastic response from the royals.
For more from Pitt this awards season, watch the clip below: