"When Villas-Boas went to spend a weekend in London over a month ago, I spoke to Pereira about his availability and he said yes, so on Friday I told him the appointment would become a reality," Porto president Jorge Pinto da Costa told reporters.
Villas-Boas earlier on Tuesday paid a 15 million euro release clause to resign from his post, with Premier League Chelsea later saying they hoped to agree personal terms with the 33-year-old coach soon.
Pereira, 42, who joined Porto as Villas-Boas' assistant in June last year, has signed a two-year contract as head coach.
"It's a natural succession and that was planned for a while, since it is obvious that what happened is part of life, and we knew that for some time," Pinto da Costa added.
"We hope once again to continue the wave of victories that has marked Porto teams in recent years."
Prior to working with Villas-Boas, Pereira managed clubs in the lower divisions of the Portuguese League and spent two seasons in charge of Porto youth teams.
The pair were hugely successful immediately, guiding Porto to the Portuguese Premier League title undefeated and also winning the Europa League and the Portuguese Cup.
Pereira said Villas-Boas had invited him to join the coaching staff at Chelsea, but that he opted to stay at Porto, where he believes the team can continue winning.
"Many great coaches made history here. Villas-Boas made history, in which I am proud to have taken part, but the past is the past and we will certainly keep winning," Pereira said.
He said his main task would be to retain the league title.
Media reports in Portugal have said profilic Colombian striker Radamel Falcao and influential midfielder Joao Moutinho may follow Villas-Boas to Chelsea, but Pinto da Costa said Porto had not received any offers for players.
