Emery was among five nominees for the honour, alongside Spain's Luis de la Fuente, Paris Saint-Germain's Luis Enrique, Bayern Munich's Vincent Kompany and Arsenal manager Mikel Arteta.
The award ultimately went to De la Fuente following an outstanding year with Spain, which culminated in the national team's victory at the 2026 FIFA World Cup.
However, Vidagany believes Emery's achievements at Villa Park deserved greater recognition, particularly after the Spaniard guided the club to its first major trophy in 30 years.
Aston Villa secured the Europa League title in May with an emphatic 3-0 victory over Freiburg in Istanbul.
Goals from Youri Tielemans, Emiliano Buendia and Morgan Rogers completed a memorable evening for the club, which had not lifted major silverware since winning the League Cup in 1996.
The triumph also represented a remarkable achievement for Emery, who became the first manager to win the UEFA Cup or Europa League with three different clubs.
The Villa manager had previously claimed the competition three times with Sevilla and once with Villarreal before adding a fifth triumph to his personal collection in Istanbul.
Vidagany subsequently took to social media to express his support for Emery, while acknowledging the collective nature of football and the contributions made by everyone associated with the club.
"I am not a big fan of individual awards because football means teamwork and family and belonging to something greater," he wrote.
"But Unai represents his own excellency and the hard work and effort of hundreds of men and women with a purpose in Aston Villa. From owners to staff.
"Unai didn't win but he deserved with my high respect to Luis De la Fuente, also a fair winner."
Vidagany's comments reflected the importance Villa place on Emery's contribution to their transformation since his appointment in November 2022.
The Spaniard inherited a side struggling near the Premier League relegation zone following Steven Gerrard's departure.
Since then, he has established Villa as a regular contender for European qualification, taking them into the Champions League quarter-finals in 2025 before delivering the Europa League trophy the following season.
The club's European success was particularly significant given the length of their wait for another major honour.
Vidagany also used his message to praise sporting director Roberto Olabe, suggesting that the individual recognition should extend beyond the manager to the people responsible for building the club.
"And if there will be one for the best sporting director it would be for Roberto [Olabe]. Keep going guys. Our Ballon d'Or is what we are building. UTV."
His reference to Olabe underlined Villa's belief that their progress has been the result of a wider sporting project rather than the work of one individual.
Emery was not the only Villa representative at the ceremony.
Young midfielder Johan Manzambi was also nominated for the Men's Young Talent of the Year award, although that honour went to Barcelona's Lamine Yamal.
The evening therefore provided Villa with recognition on an international stage, even if their representatives left without collecting the individual awards.
For Vidagany, however, the club's ambitions and continued development remain more important than individual honours.
Emery has already delivered a historic European triumph and will be expected to build on that achievement as Villa attempt to establish themselves among England's leading clubs.
The director's message was ultimately one of appreciation for the manager and the wider organisation, with the club's progress providing its own measure of success.