The Championship play-off final will still be at Wembley on May 30, the traditional Bank Holiday Monday slot, two days after the Champions League final is played in the evening at the same venue.
The League Two final will be on May 28 with the League One final on May 29 at Manchester United's ground, and all three play-off matches are scheduled to kick-off at 3pm.
Football League chairman Greg Clarke said: "We are thrilled to have the opportunity to play these exciting winner-takes-all occasions at one of the great stadiums in world football.
"We are equally pleased that we are able to take the npower Football League play-offs to the north west, an area that has been at the heart of professional football since its very origins."
Manchester United chief executive David Gill added: "We are delighted Old Trafford has been chosen to stage these two finals."