The duo had taken to the stage to accept the award for 'Best Video' and West stepped up to the microphone to say thank you.
However, Jay-Z stepped in and said: "Excuse me, Kanye, I'm going to let you continue, but..."
The joke was a reference to a controversial incident in which West interrupted Taylor Swift at the 2009 VMAs to say that the award she had just won should have been given to Beyoncé.
At last night's ceremony, West appeared to take the joke well and hugged Jay-Z before continuing with his acceptance speech.
The duo had beaten Beyoncé in the category, prompting her to playfully hit her husband Jay-Z before he took to the stage.
Meanwhile, West's girlfriend Kim Kardashian later took to her Twitter page to congratulate him on his success at the awards.
Watch Jay-Z interrupting Kanye West at the BET Awards below: