The Gunners will now face one of the group winners after next Friday's draw for the last 16 of the competition is made.
In truth, Arsene Wenger's side were fortunate to return to London with only a two-goal defeat such was Porto's dominance, particularly in the second half.
Wenger named a young side that included Emmanuel Eboue, who had been booed mercilessly by Arsenal fans in Saturday's win against Wigan Athletic.
Aaron Ramsey and Carlos Alberto Vela also started but a repeat of Arsenal's 4-0 victory against the Portuguese side at the Emirates Stadium in September was always unlikely.
Arsenal started brightly enough after Porto's Brazilian striker, Givanildo Vieira Hulk, had an early sniff of goal that William Gallas and Manuel Almunia cleared up.
When the visitors responded, Denilson's lofted free-kick caused some consternation in the Porto defence before they cleared the ball.
At the other end Bruno Alves' free-kick beat the wall but Almunia got down well to claim the ball but it was a very scrappy start to the game.
In the 25th minute a good Arsenal move ended with Ramsey's fierce left-footed drive being palmed away for a corner by Helton. Four minutes later Gallas got in a muddle allowing Lisandro Lopez to bear down on Almunia who did well to keep the powerful shot out.
However, Porto took the lead in the 39th minute with a simple goal. Abou Diaby was day-dreaming as a corner was floated in, allowing Bruno Alves to power a seven-yard header past a stranded Almunia.
Porto's dominance continued after the break and they could easily have added a hatful of goals.
The only one they managed in the second half came in the 54th minute when poor positioning by Mikael Silvestre allowed Lisandro Lopez to surge clear before powering an unstoppable shot past Almunia.
Cristian Rodriguez twice fired well as Porto counter-attacked with pace and Lucho Luis Gonzalez clipped a shot wide when he should surely have hit the target.
But Porto had already done more than enough to clinch top spot in the group while Arsenal's inconsistent season has taken yet another dip.