He was the second son of Johann Ernst II, Duke of Saxe-Weimar, and Christine Elisabeth of Schleswig-Holstein-Sonderburg.

After the death of his father in 1683, he inherited the duchy of Saxe-Weimar with his older brother Wilhelm Ernst as co-ruler (Mitherr).

Johann Ernst was an alcoholic; this, and his non-interest in the government, was taken advantage of by his brother, who became the only, autocratic, ruler of the duchy.

In the first half of 1703, Johann Sebastian Bach served as a court musician at Weimar.

They had five children: In Kassel on 4 November 1694 and only two months after the death of his first wife, Johann Ernst married secondly Charlotte Dorothea Sophia of Hesse-Homburg.