Johnson, who had a global hit with Get Get Down in 1999 and was named as an influence by Daft Punk, had spent several weeks in hospital.
A statement on his Facebook page read: "Our greatness passed away this morning at 9am, the house music legend we all know as PJ aka Paul Johnson."
Fellow DJ Mike Servito said Johnson "taught us how to bounce to the beat".
Mixmag posted: "House music has lost an all-time great."
The late DJ and producer, who started out as a break dancer, became a key figure in the second wave of Chicago house music in the mid 1990s, and was the first name mentioned on record by Daft Punk as one of their Teachers.
Get Get Down reached number five in the UK chart and was a club anthem.
Johnson had been shot in 1987 and his injured leg was later amputated. He lost his other leg in 2010 following a car accident.
In an interview in 2014, he said: "I never think about me when I'm spinning - just the people who are dancing.
"The crappy life I've had health wise, that's been nothing, man. That's just been a shadow to what I've been doing, I don't even see it, nobody sees it. It's all about the music."