The win lifts the Portuguese champions to top the group with 12 points, while Arsenal are demoted to second with eleven.
The home side goals came through Bruno Alves on 39 minutes and Lisandro in the 50th minutes.
Porto were given a controversial penalty as a result of what seemed a fair tackle by Nicklas Bendtner on Alves. The Brazilian stepped up and successfully turned the ball in the back of the Arsenal net.
Lisandro added Porto’s second on 50 minutes, as he caught Arsenal’s backline napping with a staggering shot.
In the same group, Dynamo Kiev clinched a UEFA Cup berth after beating Turkey’s Fenerbahce 1-0.
Roman Eremenko’s strike was enough to win the game for the Ukrainian outfit.
The attacking midfielder capitalized on a counter attack lead by Artem Milevsky who passed towards Ermenko, and the latter took advantage by firing a powerful shot from the edge of the Fenerbahce box.
Dynamo are now in third place with eight points, six adrift of Fenerbahce.