The left-back is thought to have been involved in an incident involving captain Doug Loft last week as Vale prepared for their League One fixture against Notts County.
Both players were left out of manager Micky Adams' squad for the game on Saturday, which the Valiants lost 4-2.
After the match at Meadow Lane, Adams revealed that a facial injury sustained by Loft was so severe that he will miss the rest of the season and that the club were conducting an internal investigation into the events.
As a result of that investigation Jones has had the remaining year of his contract cancelled.
A statement on the club's official website said: "The club has today (Monday) announced that defender Daniel Jones has left Port Vale with immediate effect.
"Nothing further will be said on the matter at this time."
Jones, 27, formerly of Wolves and Sheffield Wednesday, signed a new two-year deal at Vale Park last summer.
Loft's current contract with the club is set to expire at the end of the current campaign.