Vedad Ibisevic's 23rd-minute penalty and a close-range finish from the influential Ondrej Duda on the stroke of half-time condemned the Bundesliga champions to a 2-0 loss, following a second underwhelming performance in succession.
“We were not 100 per cent present in the first half,” he told reporters after the game.
“The issue of missing opportunities remains a big one – this was the case again [against Hertha]. We were optimistic at half-time that we could still turn it around.
“In the Champions League everything is possible because we won the first game [against Benfica].
“We are all professional enough and know what football is like.”
Since joining from Schalke in 2011, Neuer has helped oversee a new golden era for Bayern, starring in goal as they claimed six consecutive Bundesliga titles, beginning with a treble triumph in 2013 that saw them also win the DFB-Pokal and the Champions League.
He also won the 2014 World Cup with Germany, but endured a poor tournament in Russia as captain of the national team, with the defending champions eliminated at the group stage following defeats to Mexico and South Korea.
Following their game against Ajax, Bayern return to domestic duty with a fixture against Borussia Monchengladbach on October 6, before a fortnight hiatus for the international break.