The 50-year-old last week intimated at a possible fix in determining the winner of the accolade Vicente del Bosque, but the world governing body insisted that the FYROM captain nominated the Spain boss, releasing an image of his ballot paper.
"Pandev was one of those that called me. Others prefer to remain anonymous, and I can only respect that. I appreciate Goran's honesty and strength," Mourinho said at an event in his hometown, Setubal.
"My intention was to explain why I didn't attend the gala, not why I didn't win. I probably wouldn't have won it anyway, but things are now clear to me and no-one can criticise me, period!"
Pandev had insisted that the ballot paper Fifa published was not his own: "All I can say is that the signature that appears on the fax is not mine. Jose Mourinho was my choice. Everyone knows that," he told Calciomercato.
"We all know strange things go on here, but we can't change the way it is. Neither me nor Mourinho can."
And in another twist, Fifa released an official statement to challenge Pandev's integrity, claiming that the ex-Lazio man should demand an explanation from his country's football association.
"If Pandev doesn't recognise his vote, he should hold his country's federation accountable, not us," it said.