Poland international Lewandowski, 24, was shown a straight red card during the 4-1 defeat to Hamburg earlier in February after clipping Norway midfielder Per Ciljan Skjelbred late as they contested a 50-50.
Dortmund claimed the red card was excessive and that it was a yellow-card offence, but - despite Skjelbred giving evidence in favour of his opponent - the ban was upheld.
The club could technically launch a second appeal but are unlikely to do so.
Having already sat out the match against Eintracht Frankfurt, Lewandowski will miss Bundesliga clashes with Borussia Moenchengladbach and Hannover 96.
Dortmund CEO Hans-Joachim Watzke was disappointed with the decision.
"The previous claims (of the DFB) were refuted in court, but the sentence was confirmed. We may as well not have stayed at home," said Watzke.
"We believe that the findings of today's evidence should have led to a different result. Yet such appeals seem to be pointless.”