Coming off a 6-0 drubbing at Chelsea on Saturday, the Gunners endured another demoralising result after rallying for a 2-1 lead only to concede a late equaliser.
Vermaelen felt match fitness was not an issue as they allowed the visitors to dent their title ambitions in stoppage time.
"The most important thing today was to react well after the defeat on Saturday and get a good result. We worked hard for it, but in the end 2-2, we're not happy with that," the Belgian defender told Sky Sports.
"We were pushing the whole game and then playing in their half to score the first equaliser and then to take the lead.
"After that they had more possession even though we wanted to keep the pressure on them and try to score a third goal but they came back into the game and made it 2-2.
"We just had to make sure that we didn't score a goal from the counter-attack. It's just being patient and although we scored twice, they scored right at the end as well.
"Of course we're missing players but we have a big squad with lots of players so that shouldn't be the reason.
"I don't think there was a lack of confidence in the team. We were pushing the whole game and we had most of the possession. We tried very hard so in the end it was a disappointing result."