The 27-year-old defender is understood to have confronted Doug Loft last week, leaving the Vale captain with facial injuries that will keep him out for the rest of the season.
Jones has now had his contract terminated after an internal investigation by the League One club.
"The club has today (Monday) announced that defender Daniel Jones has left Port Vale with immediate effect," read a statement on Vale's official website. "Nothing further will be said on the matter at this time."
Jones signed a new two-year contract at Vale Park last summer.