The father of two only recently had requested that his birth certificate reflect the sex change, but chose not to be divorced from his spouse.
The Austrian Constitutional Court did not object to the transsexual's request.
"Changing a sex entry in a birth certificate cannot be hindered by marriage," the court said on its Web site.
By allowing the entry change in the man's birth certificate, it automatically lifted a former order imposed by the Interior Ministry.
In 1996, the Interior Ministry issued a transsexual law, which stipulates that partners of the same sex must not be married, according to the AP.