The DR Congo defender was a key part of Benitez's plans at the end of last season, starting the last nine Premier League games.
The 21-year-old impressed after his summer move from Anderlecht, but was unable to stop Newcastle from slipping into the Championship.
He has since been linked with a move to Italian side Fiorentina, but he has intimated he is prepared to stay at St James's Park after Benitez committed his future to the club.