Jovanovski was named Bangladesh coach on June 14, replacing Croatian Robert Rubcic who was axed after a pay dispute.
Jovanovski's first assignment was to lead the team in the two-leg Asian zone preliminary round tie against Pakistan on June 29 in Dhaka and July 3 in Lahore.
He was set to join up with the team on Monday but the former Yugoslavia international delayed his arrival and told the Bangladesh Football Federation that he would arrive after the tie had been completed.
"We have no choice but to cancel his appointment as he is unwilling to travel to Pakistan," said Badal Roy, chairman of the national team management committee.
Jovanovski's compatriot Nikola Ilievski was named as his replacement on Thursday.
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