Madueke opened the scoring with an unstoppable strike after 27 minutes before he headed into an empty net just 80 seconds into the second half.
Gabriel Martinelli put the game out of reach when he scored a wonderful third 10 minutes later.
- Champions League recap: Madueke, Martinelli steal show for Arsenal
Despite reluctance from some Arsenal supporters over Madueke's arrival from Chelsea, the £50 million ($67m) man has impressed for his new club and his two-goal haul on Wednesday comes a fortnight after he opened his account in a 3-1 win against Bayern Munich.
"It was an unbelievable goal," said Arteta as he reflected on Madueke's first-half thunderbolt.
"When you talk about individual quality and individual action and magic moments, that's it, for a player to be able to pick the ball that far, dribble past people and finish with the quality and the power that he's done.
"At this level, you need individual players to step up and to do something different. So I'm very happy because now we have some players back in the front line and you can tell how much better we are with them."
Bukayo Saka has made the right-hand side of Arsenal's front three his own but Madueke's form provides Arteta with a dilemma of sorts.
Asked if Madueke is now undroppable, Arteta continued: "It's about consistency.
"It's not about one game, two games, three games, it is when you do it 10 games in a row, every three days and that's the level that we have to hit. That's the challenge for him."
Despite being unable to select eight injured players -- with Jurriën Timber unavailable despite travelling to Belgium -- Arsenal followed Manchester United, Leeds, Liverpool and Manchester City in becoming the fifth English team to win all of their first six European Cup matches.
The top eight are assured of automatic qualification to the last 16 and Arsenal, the only team with a 100 percent record so far, are six points clear of ninth-placed Liverpool with a superior goal difference of 13.
Gabriel Jesus ended his 332-day injury exile when he replaced the ineffective Viktor Gyökeres on the hour mark.
Jesus, who has been sidelined since rupturing the anterior cruciate ligament in his left knee on Jan. 12, came within inches of capping a brilliant evening for Arsenal only to see his right-footed strike cannon off the woodwork.
"It's been a very, very difficult and long journey for Gabi," added Arteta.
"For 11 months, he's been fighting against another very difficult injury and to see him back with that smile, with that energy and with that quality in his first performance back with us is really impressive and we're all delighted for him. You can see how much we love him!
"If he continues to perform in that manner, he will bring something else to the team and I am really happy to see that."
