Braga's run as Portuguese leader lasted just five days as a stoppage time goal saw it lose 2-1 to Benfica on Saturday, allowing Porto to go back to the top.
Bruno Cesar scored a 92nd-minute winner that lifted Benfica into second ahead of Braga, which saw its winning streak end at 13 games.
Porto leads Benfica by one point and Braga by two after a 2-0 triumph over Olhanense, although the standings could reshuffle again next weekend when the defending champion travels to Braga. Benfica plays Sporting Lisbon in a city derby in the next round.
Cesar was fouled inside the Braga area to set up Benfica's opener, as Axel Witsel converted a 78th-minute penalty by sending goalkeeper Quim the wrong way.
Braga equalized in the 82nd when Hugo Viana's free kick into the area sailed through the hands of Benfica keeper Artur Moraes to reach Elderson Echiejile, who redirected the ball in at the far post.
Braga remained winless at the Stadium of Light since the 1954-55 season, however, after Nicolas Gaitan ran inside the area from the right before cutting a pass back to Cesar, who rolled a shot past Quim inside the far post.
Lucho Gonzalez and James Rodriguez scored either side of halftime for Porto at its Dragon Stadium.