Roux stepped down earlier this year as a result of a dispute with the BBC about his endorsement of a brand of potatoes.
Wareing - who has two Michelin stars and has worked at some of the world's top restaurants - joins Monica Galetti and Gregg Wallace on the judging panel for the seventh series which returns in the autumn.
He said: "I have been watching MasterChef since I was a young kid at catering college and in more recent years I have enjoyed an established relationship with the programme.
"To now become part of the show is hugely exciting for me; to be asked is a true honour. Michel has left big shoes to fill and I am delighted to be working with Monica and Gregg on a new journey of discovery to find the next generation of Michelin-starred chefs."
Wareing began his career at 18 working at The Savoy and went on to be awarded his first star seven years later.
Wallace said: "One of the outstanding chefs of my era - I'm absolutely thrilled to be working with Marcus."
Karen Ross, the creative director of the production company behind the show Shine Soho, said: "We are delighted that he is taking up the baton of judge with us - his experience of coming from humble beginnings in the North of England and making his way into the country's best kitchens, to then rise to be awarded two Michelin stars is extremely inspiring and will speak to the young chefs who hope to follow in his footsteps."