The 19-year-old midfielder has played an instrumental role in Tottenham's bid for a first league title for 55 years, scoring seven goals and claiming nine assists in 27 league appearances, as well as earning a first England cap.
He has also suffered knee and ankle injuries, however, and although now fully fit, his suspension from the round of 16 first-leg game in Germany on Thursday gives him the chance to rest before Spurs play bottom club Aston Villa on Sunday.
"He is an incredible athlete, yes. But he is not a machine. He has had problems with his ankle and knee," Pochettino said after Spurs drew 2-2 with Arsenal on Saturday.
"We have different plans for different players, we analyse the minutes they play and how they are."
British media had reported that Alli was playing in pain for the Tottenham cause but the club clarified the situation.
"He is fully fit," a spokesman said. "He had some injuries which have now cleared up, but will miss the Dortmund game after three yellow cards in the competition."
Pochettino's side are second in the Premier League table, five points behind Leicester City with nine games left.
(Reporting by Shravanth Vijayakumar in Bengaluru; Editing by Ed Osmond)
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