Rybakina, a former Wimbledon champion, is looking to improve on her best performance of quarter-finalist on the Paris red clay, back in 2021.
The Russian-born Kazakh lost her serve twice in the first set but maintained the upper hand by breaking all of the Belgian's remaining service games in the set.
Strong shots and better serving in the second set allowed Rybakina to end the match in little over an hour.
"In the second set I was playing with a bit more confidence and my serve improved," Rybakina said.
The two women had met five times previously, with the Kazakh leading by four wins to one.
In the fourth round, Rybakina will face Ukraine's 19th-ranked Elina Svitolina or 64th-ranked Romanian Ana Bogdan.