Galatasaray dominated the match until Micael put the visitors ahead in the 27th minute after Antonio Eder penetrated the Turkish side's defense and passed the ball to Ruben Amorim, whose shot was blocked by goalkeeper Nestor Fernando Muslera. The ball fell to Micael, who knocked a low shot into the empty net.
"We were the dominant side until the 27th minute," Galatasaray coach Fatih Terim said. "We were a team which controlled the ball but weren't able to find the goal that would have enriched the game."
Braga grew in confidence after the goal but wasted a couple of good chances to increase its lead.
"They put us under intense pressure from the first minutes," Braga manager Jose Peseiro said. "Our defense was strong. We would have liked to have controlled the ball more. (But) I believe it was a deserved win."
Galatasaray fought back in the second half and Burak Yilmaz provided the biggest threat to the visitors with several long-range efforts at the Braga goal. But it was Aydin Yildiz who came closest in the 77th minute with a powerful shot that was tipped onto the crossbar by Braga goal keeper Antonio Beto.
"We started the second half well. We were again the dominant side, but it wasn't to be. Again we were unable to score," Terim said.
In the fourth and final minute of injury time, Alan secured the win on a counterattack after taking a pass from the left.
"We played well. It wasn't easy, the (Braga) defense was strong," said Galatasaray's Ivory Coast international, Emmanuel Eboue.
Both teams had lost their previous matches in Group H, which also includes Manchester United and Romanian champion Cluj. United leads the group after beating Cluj 2-1 on Tuesday.
The game was the first Champions League match at Galatasaray's 50,000-capacity Turk Telekom Arena.
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