Arsenal made eight changes and took to a back three for more defensive solidity in this 1-1 draw. That was a bridge too far in the first half as the players were unsure of positions on the pitch.
Vitoria started brightly with Martinez having to save two shots.
Arsenal replied with a dangerous cross from the right from Maitland Niles and the left from Saka.
Vitoria were winning turnovers in midfield and finding a lot of unmarked space in front of the back three, taking to shooting outside the area.
The Vitorian Pepe took a good shot – which hit the post and ex-Spurs trainee Edwards had a shot well saved by Martinez.
A free kick into the Arsenal area saw Tapsoba flick a header goalwards, but the Argentine goalkeeper tipped it over.
Arsenal held a high line from set piece free kicks – but didn’t defend the second ball on the edge of the area. Maitland Niles was caught out of position on the left, followed swiftly by Mustafi who was booked for dragging back.
Vitoria started persistent fouling with only one booking.
At the beginning of the second half, Martinelli linked well with Saka but the effort came to nothing.
Edwards ran to the byline but was blocked by Ceballos who ran the length of the pitch to clear. But that was a run too far as his next move saw him clutching his hamstring. He failed to run it off and was replaced with Guendouzi, injecting more energy and direct running.
Arsenal tightened up defensively and exerted more control in midfield.
But the game was littered with misplaced passes and fouls.
Mustafi had a good chance from a set piece but headed over. Saka was disposessed on a number of occasions and was substituted for Lacazette with Martinelli moving to the wing.
Some of the referee’s decisions were the homer type, for example booking Holding, captain for the evening for a 50/50 tangle.
Willock found some space running to the Vittoria goal – but shot way over the bar.
Arsenal won a free kick and up stepped Pepe, to show a bit of dead-ball quality with a curving ball met forcefully by Mustafi arrowing its way into the corner of the net. That will do him some good.
But this is Arsenal. And in the second minute of injury time Edwards ran to the byline with Holding backing off, crossed and the returned header found Duarte who bounced an overhead volley into the net.
Soon after a cross shot hit Mustafi and brushed the post.
It was the sixth time in ten days that Arsenal had lost a lead. But with negatives come positives and the club remain top of their group with every chance of finishing top.
Vitória Guimarães: Renato de Jesus, García, Venâncio, Tapsoba, Soares (Booked at 33), Agu, Edwards, Evangelista (Substituted for Bonatiniat 82),Figueiredo Rodrigues (Substituted for Pohaat at 61),Pereira (Substituted for Rochaat 68),Duarte da Silva
Arsenal: Martínez, Mustafi (Booked at 18), Papastathopoulos, Holding (Booked at 66),Maitland-Niles, Willock (Substituted for Torreira at 78), Ceballos (Substituted for Guendouzi at 54), Tierney, Pépé, Martinelli, Saka (Substituted for Lacazette at 65)