Heaton, 24, spent the 2008/09 season on loan at Cardiff and has struggled to make an impact at United after falling further down the pecking order with the emergence of young keeper Ben Amos.
The limited opportunities in goal for United also saw Ben Foster join Birmingham last month and Heaton will leave the Red Devils without a first team appearance after joining the club at 16-years-old.
Further loan spells at QPR, Rochdale and Wycombe last season convinced the England under-21 shot stopper to move away from Old Trafford for regular first-team football.
Cardiff boss Jones said: "I'm pleased that we have secured Tom's services from Manchester United.
"We all know about the lad from his time on loan here and know that we have signed a very talented young player.
"United had offered him a new contract, but Tom's attitude was that he wanted to play, which says a lot about him as a player and a professional. He will certainly be a welcome addition to our ranks."
But Jones feels Heaton will have to work hard to get a starting place in his competitive side, who just missed out on a Premier League place in the play-off final against Blackpool.
He added: "It's now a case of Tom and Dave [Marshall] working hard with our goalkeeping coach Martyn Margetson, battling to claim a starting place in the squad.
"We look forward to seeing him for pre-season training and know that we have a real prospect for years to come."
By Saad Noor
