Seydou Doumbia scored the first goal of this season's Champions League early on, latching on to a cross from the right to give his side the lead.
Gelson Martins made it 2-0 after just 13 minutes as the visitors took complete control of the game. That control led to the Portuguese side extending their lead further just before the break, with Bruno Fernandes tucking home the third.
At that point, you could have been forgiven for thinking the game was over but the hosts improved noticebly after the break.
Despite their improvement, it took them until the 89th minute to give themselves a glimmer of hope with Felipe Pardo reducing the arrears.
Late in added time Pardo added his second but in the end it was too little too late for the Greek side, who fell to a 3-2 defeat.