Rob Holding captained the Gunners side that handed a start to Nicolas Pepe following his match winning double from the bench in the reverse fixture two weeks ago.
Vitoria gave the first scare inside eight minutes when Pepe's long range drive cracked the face of the post after opening space outside the danger area.
The Gunners remained on the back foot before the 20th minute spell as Edmond Tapsoba went close with a glancing header from a free-kick on the near side.
Vitoria went close again five minutes before the half-hour mark as Davidson Pereira curled wide of the far corner after founding space in the six yard area.
The visitors well documented struggle across all phases raged on at the start of the second half, with Vitoria maintaining the balance in defence and attack.
A hamstring injury for a certain Dani Ceballos on the 54th minute spell signaled his removal for Matteo Guendouzi in the middle of the park.
Unai Emery's side struggled to open up the Portuguese side despite the promising moves, thus giving the Spaniard no choice but to bring on Alexandre Lacazette after 65 minutes.
The Frenchman's arrival signaled a change for the visitors in the final ten minutes as Shkodran Mustafi connected with Pepe's free-kick to head in the bottom near corner.
Vitoria levelled in the first minute of added time through an overhead volley from Bruno Duarte after the Gunners failed to clear their lines.
The Gunners almost succumb to a second within the matter of minutes, but honours even was how the contest played out in Guimaraes. Emery's charges will qualify for the last 32 if Eintracht Frankurt beat Standard Liege on Thursday.