The Nerazzurri lost 2-1 at Werder Bremen on Tuesday and finish the group second behind Panathinaikos.
“We heard the result from Athens and knew we just had to end the match with dignity,” said Mourinho.
“I think that by finishing this group with eight points, we fully deserve to face one of the strongest sides in the next round.”
He continued: “This match to be is not a reference point, as we did not play with our best XI. Tonight Bremen were a top class side and they were the ones expected to go through, not Panathinaikos.
“Whatever team comes in second of their group and picks Panathinaikos is the luckiest club in the draw.
“In Serie A we are focused, concentrated, strong and hungry. After our qualification campaign, we deserve to face Barcelona, Manchester United or a side of that calibre. We got ourselves in this situation.”