Villas-Boas, 46, received 21,489 votes compared to just 5,224 for his opponent, 86, who had led “The Dragons” in 15 straight elections prior.
“What a historic night. Our club is alive, and today proved its strength,” Villas-Boas said in a Porto statement.
At Porto, Villas-Boas had his most prosperous tenure as manager.
At the young age of 33, he led them to victory in both the Portuguese Cup and the Europa League during the 2010–11 season, as they emerged as domestic champions without dropping a single match.
After defeating Portuguese rivals Braga in the Europa League, he became the youngest coach in history to win a European club title at the age of 33 years and 213 days.
During his campaign, Villas-Boas stated that he would appoint Andoni Zubizareta, a former Spanish international goalkeeper whom he had met while managing Marseille in Ligue 1, to the position of sporting director.
In addition, he promised to appoint former Portugal international defender Jorge Costa to lead the football division.
Sergio Conceicao, the current head coach, got his contract extended this week by Pinto da Costa.
Porto has had unheard-of prize success since Pinto da Costa was first elected in 1982, taking home 23 league trophies, the 1987 European Cup, and the 2004 Champions League.
But things have taken a bad turn this season.
The squad has struggled on the field and is beset by financial issues. They are now in third place in the league rankings, eighteen points behind leaders Sporting, whom they will meet later on Sunday.
After retiring from coaching in 2021, Villas-Boas will face a fresh task as he concentrates on the presidential race after his turbulent tenure at Marseille concludes.
In contrast to his countryman and former Porto coach Jose Mourinho, he did not live up to the early expectations despite holding prominent positions at Chelsea and Spurs.
He barely made it through one season at Spurs and less than one at Chelsea.
After that, spells included China, Russia, where he led Zenit St Petersburg to the Russian Cup (2016) and league victory (2015), and the disastrous journey with Marseille.