On 20 April 1873 she was married to Prince Leopold of Bavaria in Vienna, a son of Prince Regent Luitpold of Bavaria and Auguste Ferdinande of Austria and second cousin to Gisela.
According to a letter to his mother written in 1872, Emperor Franz Josef wanted the match between his daughter and Prince Leopold as there were so few Catholics princes available at that time and they had to secure the only one to whom they could give Gisela (whom he called "our darling girl" during the wedding rites) with confidence. A year later she gave a birth to her first child Elisabeth Marie and had four children in total. She was made welcome in Munich by her husband's family and lived in the Palais Leopold in Schwabing where the street opposite the Palais was named Giselastraße in her honour in 1873.
Gisela and Prince Leopold of Bavaria had four children:
Princess Elisabeth Marie of Bavaria (1874–1957), who married Otto Ludwig Philipp Graf von Seefried auf Buttenheim
Princess Auguste Maria of Bavaria (1875–1964), who married Joseph August, Archduke of Austria
Prince Georg of Bavaria (1880–1943), who married Archduchess Isabella of Austria
Prince Konrad of Bavaria (1883–1969), who married Princess Bona Margherita of Savoy-Genoa
Gisela and her husband celebrated their golden wedding anniversary in 1923. Her husband died in 1930 and Gisela only survived him by two years and died aged 76 in Munich on 27 July 1932 and is buried next to Prince Leopold in the Colombarium at the St.Michaelskirche, Munich.