Both encountered each other on Ryloth, immediately becoming enemies. Throughout the series, despite hardly interacting with each other in Rebels, Ezra developed an indifference and extreme hatred for Thrawn due to his mistreatment of his mother figure, Hera and being responsible for the death of one of his parents' friends, Morad Sumar. Seeing him as nothing more than a child rather than a deadly opponent, Thrawn completely underestimated Ezra, believing him to be a lesser opponent than any of the other ones he had faced.
The two finally interacted with each other in the series finale of Rebels, where Ezra remained defiant in Thrawn's presence, and defended the Jedi when Thrawn mocked Ezra of fallowing their same path. He was filled with rage and disgust that Thrawn had collected many artwork over the years, including Hera's kalikori, Sabine's artwork and some artworks from Lothal and told Thrawn that he didn't deserve any of it or his own homeworld. One year earlier, Bendu foresaw Ezra cause the Grand Admiral's downfall, when the Jedi called the Purgill and had them carry him, Thrawn and the Chimeara from Lothal. However, both survived the trip into hyperspace, into parts unknown. Lothal was never targeted by the Empire again, while Ezra and Thrawn continued to clash on the extragalactic world of Peridea for the next ten years until they both returned to the galaxy.