Born in Gomadingen, Kingdom of Württemberg (modern-day Germany), Auer was ordained a priest on July 25, 1858, as a member of the Congregation of the Holy Spirit (Spiritans). He dedicated his life to missionary work and was subsequently appointed by Pope Pius IX as the Vicar Apostolic of the Two Guineas on October 9, 1862. This vast ecclesiastical territory encompassed areas along the West African coast, including parts of present-day Gabon.
Auer was consecrated a titular bishop of Europus on February 2, 1863. As Vicar Apostolic, he faced considerable challenges, including the geographical expanse of his mission, the prevalence of tropical diseases, and the complexities of establishing Christian communities in new cultural contexts. Despite these difficulties, he actively worked to expand the Catholic Church's presence, establish mission stations, and provide spiritual guidance.
Bishop Auer's episcopate was relatively brief, as he died in Gabon on March 16, 1869, at the age of 36. His pioneering efforts were instrumental in laying the groundwork for the future development and expansion of the Catholic Church in West Africa.