Team spokesman Mark Harrison said yesterday that Vermuelen, 24, would be sent home after a disciplinary hearing held at the team hotel in Durham on Sunday morning.
Vermuelen failed to score in either innings in the second Test at Chester-le-Street, which ended on Saturday with an innings victory for England. England won the series 2-0.
"Mark has been warned about his conduct on a number of separate occasions during the tour, but unfortunately has not heeded that advice," said team manager Babu Meman.
"The final straw concerned an incident that took place at the end of play on the Friday of the Test.
"Mark ignored a management instruction to travel with the rest of the squad on the coach, which is a practice followed at all games to promote team morale and adhere to the security advice we have been given for the tour."
Vermuelen played in both Tests and would have remained in the squad for the one-day triangular series against England and South Africa.