Zollitsch, succeeds Cardinal Karl Lehmann, who is retiring as chairman after 21 years because of heart problems, but will continue to be bishop of Mainz.
Lutheran leaders and figures from other faiths welcomed the choice, as did lay Catholic groups and Germany's two main political parties, the Social Democrats and Christian Democrats.
Chancellor Angela Merkel praised the choice, saying "Zollitsch approaches people with great openness and addresses their needs and concerns."
Germany's 25 million Catholics are organized in 27 dioceses. The chairman of the bishop's conference speaks for them in public, but has no especial doctrinal authority.
Zollitsch, who has been an archbishop since June 2003 and already oversees the church's national payroll, has been described as a liberal. He once said he would prefer priestly celibacy to be voluntary, not a rule.
He was chosen for a six-year term by his brother bishops at a meeting in Wuerzburg.
His similarity in age and positions to Lehmann indicated a choice for continuity.
"We're theologically and personally so close that you'll find it hard to see a difference," Zollitsch said.
The bishops passed over another, more conservative candidate, Reinhard Marx, 54, who has been freshly enthroned as archbishop of Munich.
Lehmann said it would do Marx good to deal with the challenges of the new archdiocese first.
Marx's auxiliary bishop, Engelbert Siebler, said, "I expect Marx will be elected to the job in six years."
Observers said the choice also indicated a continued mood of independence among the 69 bishops towards Pope Benedict XVI, the German-born conservative theologian Joseph Ratzinger.
The Vatican's response may be gauged by the time it takes to award Zollitsch a cardinal's hat.
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