Leon replaces Louie Giglio, pastor of a megachurch in Atlanta, USA Today reported. Giglio decided not to participate in the inauguration because of controversy over remarks he made several years ago opposing gay marriage.
For Leon, it will be his second appearance at a presidential inauguration. He gave the benediction for President George W. Bush in 2005.
"I don't mind being in the bullpen; relievers are very important," Leon told the CNN Belief Blog.
In a departure from tradition, Obama has asked civil rights leader Myrlie Evers-Williams to deliver the invocation even though she is not a member of the clergy.
St. John's on Lafayette Square near the White House has been nicknamed "church of the presidents" because every president since James Madison has attended services there, although not all have been members. The parish was organized in 1815 and the building completed in 1816.