The two sides meet at the Emirates Stadium in the opening round of matches in Group H, with the Gunners tipped to make it through to the last 16.
Matheus believes Braga can progress as well from a group that also contains Shakhtar Donetsk and Partizan Belgrade, and is looking to make a strong start in London.
Having knocked out Sevilla and Celtic in the qualifying rounds, Matheus insists Braga should not be underestimated.
"We have already achieved our first success of the season by reaching the group stages of the Champions League," he said in the Daily Star.
"But that is not enough. Braga are not just going into this as tourists. Now we want to travel across Europe and win.
"Arsenal are the favourites to win the match and the group - but we can spring a big surprise.
"Nobody thought we could beat Sevilla either."
Matheus accepts that Braga are likely to come under pressure from Arsenal but he believes they can pose an attacking threat of their own.
"The key to the match for us will be to give our all and take advantage of the opportunities we get on the counter-attack," explained the 27-year-old.
"I love Arsenal's incredible attacking style, but I don't intend to suffer from it.
"I intend to enjoy it. Scoring at the Emirates would be an incredible moment for me to remember."