The new policy takes effect Jan. 1, the Fort Worth Star-Telegram reported. The authority's board approved the change Wednesday at a meeting crowded with free-thinkers and church members.
Both sides cheered the decision, the newspaper said.
The controversy began two weeks ago with ads bought by the Dallas-Fort Worth Coalition of Reason. Buses carried the message "Millions of Americans are Good Without God."
Religious groups said they were especially angry the campaign began just before Christmas. One arranged for a billboard truck to follow buses, another purchased its own ad on a bus with the atheist message and some people even urged drivers to refuse to ride buses with the atheist ads.
The authority said religious organizations can still buy ads on buses but only if the message is secular. Texas Christian University, for example, can advertise campus events.