Nazi control over the church depends upon which branch being referred to.
Protestants: Were divided into 3 different groups: The Confessional church, who did not agree with the Nazis, the Reich church, who worked with the Nazis, and the German Christians, who tried controlling the Reich church itself. In the end, the Nazis succeeded in taking away the influence of the Confessional church and ended up controlling it.
Catholic:Was eventually under full control of the Nazis. Initially, they had been given the rights to schools and the ability to keep their religion intact as long as they did not interfere politically. Soon, however, their influence was curbed as well and the Nazis had succeeded in controlling the influence of the catholic church by slowly taking their influence away.