The ban comes as the alt-right movement, which includes neo-Nazis, white supremacists and anti-Semites, are being emboldened by Trump winning the White House.
Trump on Tuesday condemned the alt-right in a New York Times interview.
Breitbart was previously headed by Steve Bannon, Trump's campaign chairman and chief strategist. The news organization has drawn criticism for promoting far-right, sometimes racist views.
Trump's appointment of Bannon was denounced by civil rights organizations and minority groups including the Southern Poverty Law Center, the Anti-Defamation League and the Council on American Islamic Relations.
Advertising companies like AppNexus sell digital ad campaigns to advertisers and then place the ads on sites that are part of the network. The company has secured deals with publishers including Foursquare, Groupon and Nasdaq.
Zeitz said the AppNexus move was apolitical and the domain can be reactivated once the content in question is addressed.
"We have no interest in turning off sites because of ideology. That's not what this is about. This is about specific content that violates the hate speech code," he said.
Breitbart has used racial slurs and derogatory terms related to sexual orientation on its site that AppNexus feared could incite violence against those groups.
While the step could reduce demand for Breitbart ad inventory and thus cost the site money, AppNexus competitors such as DataXu and OpenX Software offer comparable services, according to tech market research firm CB Insights.
The ban was first reported by Bloomberg News.