Leaders Dortmund held at home by Schalke
Dortmund missed a host of chances and twice hit the woodwork and when they did manage to find the target Neuer stood in the way with a string of fine saves.
"We did not make use of our chances and one reason was Manuel Neuer," said Dortmund coach Jurgen Klopp.
"We have to live with that. We did not win and that happens sometimes."
In front of a sell-out 80,000 crowd Dortmund were in control from the start, looking for their first league double over Schalke since the 1996/97 season.
Dortmund went into the game having won 16 out of 20 matches but were thwarted by Neuer who saved from Mario Goetze and Jakub Blaszczykowski in the first half while Lucas Barrios hit the post minutes after the restart.
The visitors, with new Ghanaian signing Anthony Annan getting his first start, struggled against wave after wave of fast-paced attacks.
Felix Magath's team did though come close late in the second half when Manuel Jurado's shot was stopped by Dortmund keeper Roman Weidenfeller and then headed away.
Then six minutes from time Germany international Goetze rounded Neuer and hit the post.