The Swiss champions rode their luck en route to a famous victory that left United in the Europa Leage after finishing third in Group C.
Old Trafford medical staff also suspect captain Nemanja Vidic sustained damaged knee ligaments before being stretchered off ahead of the half-time interval in Switzerland.
Ferguson said: "Of course we're disappointed, there's no other way you can feel. We had so much possession of the ball and so many really good opportunities in the last third of the field.
"Some of our play up to that point was very good but you have to say we let ourselves down with the finishing past.
"The Europa League is a competition I've never been in at United and it does mean one thing - Sundays right through. Thursdays and Sundays. That's got to be dealt with and it's not the best but that's our penalty for not qualifying."
Basel coach Heiko Vogel said: "It was a great campaign. Today was a final in itself but we had to put in a lot of hard work to get there.
"It's a sensation, yes, because it's not every day you beat Manchester United. Altogether, it was wonderful."
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