Match ends, Vitória Guimarães 1, Arsenal 1.
Arsenal's 100% record in the Europa League this season ended as Bruno Duarte scored a 91st-minute equaliser for Vitoria Guimaraes in Portugal.
Shkodran Mustafi had provided the Gunners with the breakthrough with an unmarked header from a Nicolas Pepe free-kick with 10 minutes to go.
But Vitoria came to life in the closing stages and former Spurs man Marcus Edwards' cross from the right caused confusion in the Arsenal defence, allowing Duarte to equalise with a scissor-kick.
The result was Arsenal's fourth consecutive draw in all competitions in a turbulent week that saw Granit Xhaka stripped of the captaincy.
Arsenal are top of Group F, four points clear of Standard Liege and Eintracht Frankfurt.
Arsenal fail to hold lead again
Arsenal manager Unai Emery made eight changes from the side that drew 1-1 with Wolves in the Premier League on Saturday, including handing the captain's armband to defender Rob Holding with former skipper Xhaka not part of the squad.
The Switzerland captain was stripped of the captaincy following an angry confrontation with home fans during the Gunners' 2-2 draw with Crystal Palace at Emirates Stadium on 27 October.
Pierre-Emerick Aubameyang, who will take over as club captain from Xhaka, and German midfielder Mesut Özil also did not travel to Portugal.
Emery opted for a change in formation with a defensive back three of Holding, Sokratis and goalscorer Mustafi, with youngsters Ainsley Maitland-Niles and Kieran Tierney adding an attacking threat as wing-backs.
But for the second time in a week the Gunners were punished late on and failed to take all three points.
In a match played in torrential rain, the first half was largely uneventful with Vitoria showing early warning signs when their midfielder Pepe hit the post with a long-range effort and Edwards forced a good save from Emiliano Martinez.
Martinez was again called into action minutes later when a Vitoria free-kick found the unmarked Edmond Tapsoba but the centre-back's flicked header was palmed away.
Vitoria keeper Douglas was not tested in the opening 45 minutes as the Gunners failed to register a shot on target despite dominating possession.
Arsenal's best chance of the first half fell to Holding after clever play down the left-hand side by 18-year-old Bukayo Saka. The skipper for the match was unchallenged as he rose to meet the cross but his header went over the bar.
In the second half the Gunners began to take control and were rewarded on 80 minutes thanks to Mustafi's header from a free-kick by Pepe, who scored twice from set-pieces against Vitoria in the final 10 minutes at Emirates Stadium two weeks ago to give his side a 3-2 win.
Another victory looked to have been sealed here but Arsenal's defensive frailties were exposed in stoppage time as Vitoria found a late surge of tempo to put the Gunners under pressure and find an equaliser, earning them their first point in the Europa League this season.
Spanish midfielder Dani Ceballos suffered a hamstring injury in the second half and has been ruled out of the trip to Leicester on Saturday by Emery.
"He has a small injury but I don't think he is going to be available this week." he said.
Man of the match - Shkodran Mustafi (Arsenal)
Arsenal travel to the King Power Stadium to face Brendan Rodgers' high-flying Leicester in the Premier League at 17:30 GMT on Saturday. The Gunners are back in Europa League action on Thursday, 28 November against Eintracht Frankfurt at Emirates Stadium.
Best of the stats
- Arsenal have won just one of their eight away games against Portuguese opposition in all European competition (D4 L3).
- Arsenal have drawn their past four games in a row in all competitions, despite the Gunners having held a lead in all of these matches.
- Arsenal's goal after 80 minutes came from their only effort on target in this match, while Vitoria's 90th-minute leveller was their only shot on target in the second half.
- Eight of Shokdran Mustafi's nine goals in all competitions for Arsenal have been headers.
- No Arsenal player has more assists in all competitions this season than Nicolas Pepe (four, level with Bukayo Saka).
- Vitoria's Davidson has had more shots without finding the net than any other player in the Europa League this season (15), with the Brazilian having a further three attempts on Thursday.
- 1Renato de Jesus
- 5Soares AlvesBooked at 33mins
- 7Evangelista Santana de OliveiraSubstituted forBonatiniat 82'minutes
- 88Figueiredo RodriguesSubstituted forPohaat 61'minutes
- 91da Luz PereiraSubstituted forCosta Rochaat 68'minutes
- 96Duarte da Silva
- 16Costa Rocha
- 18Al Musrati
- 21Ferreira Coelho Pereira
- 56Macedo Silva
- 20MustafiBooked at 18mins
- 16HoldingBooked at 66mins
- 28WillockSubstituted forTorreiraat 78'minutes
- 8CeballosSubstituted forGuendouziat 54'minutes
- 77SakaSubstituted forLacazetteat 65'minutes
- Halis Özkahya
- Shots on Target
Second Half ends, Vitória Guimarães 1, Arsenal 1.
Offside, Arsenal. Matteo Guendouzi tries a through ball, but Nicolas Pépé is caught offside.
Attempt missed. Rochinha (Vitória Guimarães) right footed shot from the left side of the box is close, but misses to the right following a corner.
Corner, Vitória Guimarães. Conceded by Shkodran Mustafi.
Goal! Vitória Guimarães 1, Arsenal 1. Bruno Duarte (Vitória Guimarães) left footed shot from the right side of the six yard box to the top left corner. Assisted by Rochinha with a headed pass.
Attempt missed. Léo Bonatini (Vitória Guimarães) right footed shot from the centre of the box is too high. Assisted by Bruno Duarte.
Matteo Guendouzi (Arsenal) wins a free kick in the defensive half.
Foul by Agu (Vitória Guimarães).
Offside, Vitória Guimarães. Rafa Soares tries a through ball, but Denis Poha is caught offside.
Attempt missed. Rochinha (Vitória Guimarães) right footed shot from outside the box is just a bit too high. Assisted by Denis Poha following a corner.
Corner, Vitória Guimarães. Conceded by Nicolas Pépé.
Corner, Vitória Guimarães. Conceded by Rob Holding.
Substitution, Vitória Guimarães. Léo Bonatini replaces Lucas Evangelista.
Attempt missed. Nicolas Pépé (Arsenal) header from the centre of the box misses to the right. Assisted by Kieran Tierney with a cross.
Goal! Vitória Guimarães 0, Arsenal 1. Shkodran Mustafi (Arsenal) header from the centre of the box to the bottom left corner. Assisted by Nicolas Pépé following a set piece situation.
Gabriel Martinelli (Arsenal) wins a free kick in the attacking half.
Foul by Lucas Evangelista (Vitória Guimarães).
Substitution, Arsenal. Lucas Torreira replaces Joe Willock.
Foul by Shkodran Mustafi (Arsenal).