Eleven minutes later, though, Assifuah was penalised for committing a foul in the box and Josue managed to send goalkeeper Andris Vanins the wrong way before firing the ball through the middle from the penalty spot.
Braga resumed their lead on aggregate, but they could not celebrate for long as three minutes later Gekas nabbed a second goal by drilling the ball to the inside of the right post after connecting for the rebound.
The hosts tried to respond immediately through Josue, who found space on the edge of the penalty area before unleashing a shot towards the bottom left corner, but the keeper pulled off a save.
At the other end, Edmilson Fernandes came close with a 20-yard effort, but his attempt fell just wide of the left post.
Both sides had opportunities to score again, but the home team managed to hold on to ensure their place in the next round.