Arsenal edged victory over Thun, who offered stubborn resistance to the already-qualified Londoners despite having Armand Deumi sent off. The defender was dismissed on 35 minutes after a professional foul on Robin van Persie just outside the box.
And it was Van Persie who earned the second-half penalty which Robert Pires stroked home to earn Arsenal a club record sixth consecutive European win.
It was hard on a brave Thun side, who had two goals ruled out for offside.
The second in particular looked legal as Mauro Lustrinelli got the final touch on an inswinging free-kick into the area.
And they produced their best football when they were a man down, much to Arsenal's surprise.
Goalkeeper Manuel Almunia had to be alert on a number of occasions after the interval - a different story from the opening half.
With their progress beyond the group stage ensured, Arsenal had the opportunity to rest some of their established players.
And in midfield, young Cameroonian Alexandre Song lined up with Matthieu Flamini.
It was a pairing that proved steady enough as Arsenal dominated the first-half without too much perspiration.
However, the Gunners were not producing much inspiration either.
Van Persie had the opportunity of the half but rushed his effort and his shot was comfortably beaten away.
Thun, who had barely threatened, looked to have surrendered any slim hopes of getting anything from the game when Deumi pulled down Van Persie as the Dutchman bore down on goal.
But if Arsenal expected the next 55 minutes to be an easy ride, they did not get it.
Somehow, Thun regrouped after the interval and began to trouble the Arsenal defence for the first time in the match.
Twice they penetrated and thought they had scored only for offside decisions to rule out Nelson Ferreira's and then Lustrinelli's effort.
Arsenal responded by shuffling their defence, with the woeful Pascal Cygan replaced by Lauren at left-back.
They had already been forced into a change in midfield when Song, who had been quiet anyway, picked up an injury and made way for Cesc Fabregas.
Arsenal came close to opening the scoring when Thierry Henry ran through the left but he stabbed the ball wide of the right hand post.
But they looked short of ideas and urgency and were fortunate to win a spot-kick when Van Persie went down under Ferreira's challenge.
Up stepped Pires to slot home and make it five out of five wins for Arsenal in the Champions League this season and ensure they finish top of their group.
FC Thun: Jakupovic, Orman, Hodzic, Deumi, Goncalves (Bernardi 90), Ferreira, Milicevic, Aegerter, Leandro, Adriano, Lustrinelli (Sen 84). Subs Not Used: Portmann, Duruz, Gelson, Spadoto, Faye.
Sent Off: Deumi (35).
Booked: Aegerter, Lustrinelli, Ferreira.
Arsenal: Almunia, Eboue, Senderos, Campbell, Cygan (Lauren 67), Ljungberg, Song Billong (Fabregas 56), Flamini, Reyes, Henry (Pires 70), Van Persie. Subs Not Used: Poom, Bendtner, Djourou, Lupoli.
Booked: Cygan, Reyes, Lauren.
Goals: Pires 88 pen.
Att: 32,000
Ref: Lucilio Cardoso Cortez Batista (Portugal).