Mourinho alleged this week that people who had voted for him for the 2012 award had their votes changed, with Spain coach Vicente Del Bosque picking up the honour at a ceremony in Zurich in January, which the Portuguese declined to attend.
He brought up the issue again at a press conference in his hometown of Setubal, where he praised Macedonia captain Pandev for publicly backing his contested version of events.
The Napoli star has insisted that he voted for Mourinho rather than Del Bosque, despite FIFA releasing an image of his ballot paper which indicated he had voted for the Spain coach.
"I would simply like to thank one of numerous others who phoned me to warn me (of vote rigging), because it's not easy," said Mourinho, confirming to reporters he was referring to and praising "the captain of the Macedonia national team".
"This person who had the honour and the strength to publicly assume when others requested anonymity."
Pandev had added weight to Mourinho's allegation on Thursday when he claimed his vote had been changed.
He told Calciomercato: "All I can say is that the signature that appears on the fax is not mine. Jose Mourinho was my choice. Everyone knows that.
"We all know strange things go on here, but we can't change the way it is. Neither me nor Mourinho can."