A late goal from substitute Valentin Stocker gave the Swiss side a surprising lead for the return leg as the Bavarian giants were unable to beat inspired goalkeeper Yann Sommer.
It was Bayern's second negative result in a row, after the goalless draw at Freiburg in the Bundesliga, and Beckenbauer admits that the club are having a hard time finding the back of the net.
"The situation has become worse, but it is not dramatic," Beckenbauer said after the match.
"Basel are always good on the road, if they score in the second leg, then we will need to score three times.
"I think it is possible that Basel score in Munich. Bayern have problems scoring.
"If [Manuel] Neuer was not there, Basel could have scored two more."
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