Braga mounted a stunning second-half turnaround as Fenerbahce's ill discipline cost them dear in a 4-1 away loss, handing the Primeira Liga side a 4-2 aggregate win in the last 16 of the Europa League.
It was Mehmet Topal's dismissal - the first of three for Fener - that swung the tie after Koka's early opener had been cancelled out by Alper Potuk on the stroke of half-time, the scorer of the away goal later given his own marching orders.
After seeing a number of chances go begging the hosts began their comeback as Josue netted a 66th-minute penalty, the winger converting after Topal had been sent off for handling inside the area.
Braga still needed another goal to progress and did not have to wait long as Nikola Stoiljkovic pounced after 74 minutes, the striker swivelling to fire beyond Volkan Demirel.
Rafa Silva added gloss to their victory in the closing minutes, while Fener's frustrations manifested in further red cards for Potuk and Volkan Sen in the final few minutes - the latter appearing to push referee Ivan Bebek after his dismissal.
The Turkish side made a lively start and had the ball in the back of the net after four minutes, but Robin van Persie's neat finish was ruled out for offside.
Slowly Braga began to enjoy some possession and after 11 minutes levelled the tie, Koka timing his run perfectly to convert Nikola Vukcevic's defence-splitting pass from 18 yards.
Van Persie should have re-established Fener's lead six minutes later as he rose unmarked to meet Caner Erkin's left-wing corner, but the Dutchman was unable to get enough on his header and it dropped wide.
With the tie wide open again both sides played with freedom, but quality in the final third was lacking as chances went begging before Potuk fired Fener level on the night on the brink of half-time.
Willy Boly was able to block Van Persie's initial header, but the ball dropped to Potuk and he lashed into the top corner to give the visitors a crucial away goal and the lead on aggregate.
Needing two goals to progress to the last eight Braga were immediately on the attack after the restart and saw Josue and Boly go close - the latter heading wide from six yards.
Josue made no mistake from the spot, though, as Topal was adjudged to have blocked Rafa Silva's shot with his arm - the defender shown a second yellow card as further punishment.
Braga's comeback was complete five minutes later as Stoiljkovic pounced on Pedro Santos' header to score his third goal of the competition, before Rafa Silva ensured their progress with a low finish under Demirel.
Fener's miserable night got worse late on as Potuk was shown a straight red card for a rash tackle on Pedro Santos and Sen picked up a second booking.