Benfica suffered defeat in their final Primeira Liga match of the season as Porto dented their rivals' confidence ahead of a crucial week.
Jorge Jesus' side wrapped up the title last month and also triumphed in the Taca da Liga against Rio Ave, who they will meet again in the final of the Taca da Portugal next Sunday.
But before that the 33-time Portuguese champions face a UEFA Europa League final against Sevilla on Wednesday as they aim to erase the heartache of last year's last-gasp defeat to Chelsea.
And they will head into that contest on the back of just their second league defeat of the season, with Porto gaining some revenge for January's 2-0 loss.
Ricardo Pereira handed Porto a fourth-minute lead before a tale of two penalties settled the contest, Enzo Perez equalising with his effort only for Jackson Martinez's 20th league goal of the season to restore the hosts' lead in the first half.
The biggest issue to be decided on the penultimate day of league action - there are three fixtures to be played on Sunday to conclude the season - was at the foot of the table, where Pacos de Ferreira were consigned to automatic relegation following a 4-2 home loss to Academica.
That left Olhanense - 3-1 losers at Vitoria Setubal - in the relegation play-off spot and they will face Desportivo Aves, one of the primary beneficiaries of the Primeira Liga's expansion to 18 teams for next season.
Pacos needed something from their match to stand a chance of survival but the occasion appeared to get the better of them in the opening 15 minutes, with Moussa Gueye and Salvador Agra putting visitors Academica into a 2-0 lead.
Bebe netted twice, including one from the spot, to level it up and take his league goals tally to 11 for tha campaign, but Gueye struck again before half-time.
Agra became the third player to bag a brace, ending the hosts' nine-year top-flight stay.
Olhanense also endured a poor start and trailed to Zequinha's second-minute goal before Federico Dionisi levelled it up.
But Per Kroldrup was dismissed for a second booking before the interval and the home side took full advantage, Frederico Venancio and Rafael Martins taking the game beyond Olhanense's reach.
Elsewhere, Belenenses beat Arouca 1-0, while Vitoria Guimaraes defeated Sporting Braga by the same margin.
The 2014-15 season will see the return of Boavista, who left the league in 2009 amid financial troubles, while promoted duo Penafiel and Moreirense will join the play-off winners in a new-look Primeira Liga.
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