"The last few years have been outstanding [in the Champions League]," the manager told reporters after his side lost 2-1 at last 16 qualifiers Basel and finished third in Group C, won by Benfica.
"It's our loss because it's the best tournament in the world, it's a marvellous tournament."
He was not happy at the prospect of more Sunday Premier League games due to participation in the Europa League, where matches are normally played on Thursdays.
"It's a competition I've never been in with United, it means a lot of Sunday games and that's not ideal. That's our penalty for not qualifying tonight."
He added: "We let ourselves down badly."
United have played in the Champions League 17 times under Ferguson and have progressed from the group stage on all but three of those occasions.
However, he had experience of the old European Cup Winners' Cup which he won with Aberdeen in 1983 and United in 1991.
Ferguson said his side had paid for their poor form in front of goal.
"Of course we're disappointed, there's no other way you can feel," he said. "We had so much possession up to the last third of the field, some of our play up to that point was very good, you have to say our finishing let us down.
"We have good young players, I have trust in my young players," he said.
"That's part of football. You have to deal with disappointment, it's been used as a motivation many times.
"These young players will feel the disappointment, they are going to have to cope with it and go on with their careers."
In contrast to Ferguson, who has won a hatful of titles and two Champions Leagues in 25 years with United, Basel coach Heiko Vogel has only had a few matches as a first-team coach.
He took over earlier this season after Thorsten Fink, who was in charge for the 3-3 draw between the sides at Old Trafford, left to join Hamburg SV.
"This has certainly not done my career ambitions any harm at all," said the German, who is still in a caretaker role until the end of the year.
He declined to comment on the differences between himself and Ferguson.
"He congratulated me for the victory and wished me all the luck for the last 16," Vogel said.
