Unai Emery hailed Nicolas Pepe's match-winning impact as "perfect" after Arsenal's club-record signing came off the bench to score a brace of free-kicks and see off Vitoria.

The Europa League tie appeared to be heading in the direction of the Portuguese side after they twice took the lead at the Emirates Stadium, only for the £72million summer arrival to hit two free-kicks – the second of which came in stoppage time – and seal an undeserved 3-2 win.

After losing at Sheffield United on Monday night, Emery launched an impassioned defence of his tenure as Gunners boss on the eve of the Group F clash.

But what followed was a below-par performance rescued by the brilliance of Pepe, who until then had struggled to live up to his hefty price-tag.

Without a goal from their first two games and with no away win in Europe since 2005, Vitoria stunned the home crowd as former Tottenham winger Marcus Edwards opened the scoring before Bruno Duarte restored their lead following Gabriel Martinelli's equaliser.

With more than one "Emery Out" banner displayed and the crowd singing for Mesut Ozil – again absent from the matchday squad – it was clear Emery's calls for patience from supporters had largely fallen on deaf ears.

But the stadium erupted as Pepe took centre stage late on.

"We are very happy for him and for us because those two goals, from two set-pieces, were perfect," Emery said of the Ivory Coast international.

"He was trying a lot of set-piece shooting on the training ground last week and I was watching his shooting.

"The most important thing is the three points and that some individual players can improve, that they can take confidence for us and for them.

"Every player, usually, they need time to adapt. Pepe is a very good player and we believe in him, totally.

"The way he's going, sometimes he feels better, sometimes it's with more difficulty on the pitch.

"He's improving and tonight those two goals are really important for us first, and then secondly for him. He's continuing the adaptation in his process and as soon as he can adapt, that's better for us."

Ozil's absence was likely to be the elephant in the room should Arsenal have failed to maintain their winning start to their Europa League campaign.

The German has now been entirely left out of the last five games but Emery would not be drawn on the continued ostracism of the club's highest earner.

"Tonight is not the day to speak about that," he added.

"I prefer to speak about the match. We have all the players who played. He's not in the squad. That is the decision tonight. Now we are going to work towards Sunday."

Vitoria remain without a point in Group F despite such a spirited performance, achieved with a lengthy injury list and a number of players rested for the weekend Primeira Liga match with Sporting.

"We are sad," admitted defender Frederico Venancio after the game.

"Losing a game in the last second is hard on any team, especially after the excellent performance we made.

"We worked well, in a fantastic stadium and under a fantastic environment. Unfortunately, tiredness got the better of us in the final moments and two amazing free-kicks made the difference."