Verbeek's side are just two points above the Bundesliga relegation zone after suffering their fifth defeat in sixth matches, Felix Klaus scoring the winner for the hosts in a game that saw both teams score from the penalty spot.
Nuremberg defender Emanuel Pogatetz - who scored the opener after six minutes - was sent off in injury time of Saturday's clash for a second bookable offence.
And Dutchman Verbeek was quick to direct his anger at referee Jochen Drees, telling Sky that his side had been "playing against 12 men".
The 51-year-old also took issue with opposition boss Christian Streich, who he believed influenced the referee's decisions with "shameful, brutal and disrespectful behaviour".
And Verbeek's words have drawn the ire of the DFB, who have invited the former Feyenoord and AZ boss to explain himself before making a decision on a potential punishment.
A statement on the DFB website read: "The control committee of the German Football Association (DFB) has launched an investigation against Gertjan Verbeek. The coach of Bundesliga club Nuremberg is under suspicion for unsportsmanlike comments about referee Jochen Drees in the aftermath of Nuremberg's Bundesliga match against SC Freiburg on 29 March 2013 (2014).
"The panel has now asked Verbeek for a timely explanation. Following the receipt of the explanation, the committee will decide on the continuation of the procedure."
