The Ivory Coast midfielder suffered the ignominy of being replaced minutes from the end of the 1-0 win over Wigan on Saturday following a run of poor touches which had the crowd on his back.
Eboue had just returned from a six-week spell on the sidelines, and was only brought on to replace Samir Nasri during the first half.
Wenger admitted he removed the 25-year-old from the firing line because he feared another lapse in concentration could lead to his team conceding a costly late goal.
However, he sees no reason why Eboue should not be able to produce a performance in the Estadio do Dragao tonight, where avoiding defeat would see Arsenal — already qualified for the last 16 — through as group winners.
“Emmanuel Eboue will start,” Wenger confirmed. “He is completely in the right frame of mind.
“He was disappointed for a few days but football is magic because you have the next game and the opportunity to show how good you are.”
Wenger was also quick to remind Gunners fans of how fortunate they were to be watching such an exciting young team, one which deserved their full support during the game.
“After the game, everyone is entitled to have an opinion,” said Wenger.
“But no matter what happens, you still want your fans to be behind the team during the 90 minutes.
“I believe the fans have been swayed by scepticism from the media which has affected their belief, which can have consequences on the team. I believe they are lucky to have an extremely young team with a magnificent talent who can do extremely well.
“These players want to do well, they have the potential to do well, and they can fight against the scepticism. There is only one way for the fans to help that. You want your fans to be behind the team because they deserve it.”
Defender Johan Djourou backed Eboue to give a positive response.
He said: “Emmanuel is a strong character so he will bounce back straight away.
“You don’t want anyone to be criticised. Fans have the right to say what they think and we have to respect that, but at the same time we were a bit disappointed.”
Captain Cesc Fabregas (knee) is out and is a doubt for Saturday’s Premier League trip to Middlesbrough, which winger Nasri (ankle) will miss.
Full-back Bacary Sagna has flu, while Kolo Toure (calf), Robin van Persie (thigh) and Emmanuel Adebayor (rested) also miss tonight’s match.
However, former skipper William Gallas does return along with combative midfielder Abou Diaby.
Wenger, though, is not about to restore Gallas to the captaincy.
“Almunia will be captain because you do not want every time to change your decision again. It would be unfair to William,” he said.
Wenger, who hits another milestone as he takes his 700th game in charge of the Gunners, insists Arsenal will not be overconfident against Porto.
“Maybe Porto will play with less pressure because they are already qualified — that can sometimes make them more dangerous. We will be focused and prepared to be our best.”