Bayern won 1-0 at Signal Iduna Park to stretch their lead to seven points with six games remaining.
"We made a very good start in the opening 30 minutes but we sat too deep after that," Favre explained at his press conference.
"The second half was good too. We had opportunities, but the penultimate or final ball was missing. We at least deserved to draw.
"We played better than we did against Wolfsburg and Schalke.
"It will be very difficult in the title race. Seven points behind with six games [left], that will be brutally difficult."