A nominally Catholic country, Argentina has been a trailblazer for gay rights in the region since Peronist Fernandez legalized same-sex marriage in 2010.
Fellow Argentine Pope Francis, at the time archbishop of Buenos Aires, came out strongly against the law. The Vatican defines marriage as strictly between a man and a woman and stipulates that only those born from wedlock can receive the rite of baptism.
But as the Church loses ground to Protestant and Evangelical denominations in its traditional stronghold of Latin America, some clerics are urging an overhaul to draw believers back into the fold.
Priest Carlos Varas baptized 2-1/2-month-old Uma in the Cathedral of Cordoba, Argentina's second largest city, under the watchful gaze of her beaming parents, Carina Villaroel and Soledad Ortiz.
"Father Varas told us he had been waiting for a couple like us, a gay one, and we happened to come and he accepted us," said Villaroel on Saturday. "There's really been a social change for Catholicism to have said yes to baptizing a child from a lesbian family."
Pope Francis has said all children can be baptized, although the Church's official position hasn't changed. It was unclear if the Vatican had given its approval for Saturday's ceremony.
"While my wife and I aren't practicing Catholics, we think our daughter deserves to be baptized," Villaroel told local paper La Nacion. "We asked the president to be Uma's godmother, because it's a way of thanking her and former president Nestor Kirchner for this law that gave us rights."
Fernandez did not personally attend the ceremony, sending a representative instead.
According to Argentine tradition, the president is named the godparent of any seventh male child.
Fernandez, a fireband leftist who has championed human rights in Argentina, has expanded the custom to include seventh female children as well.
Uma's biological mother is Ortiz. Villaroel said she was sacked from her job as a police officer after requesting maternity leave.