As a given name it was mostly masculine in America until around 2009. It was already rising in popularity for girls when singer Mariah Carey gave it to her daughter born 2011 (though this probably helped accelerate it).
Eli has been used as an English Christian given name since the Protestant Reformation. A notable bearer was the American inventor of the cotton gin Eli Whitney (1765-1825).
As an English name, Caleb came into use after the Protestant Reformation. It was common among the Puritans, who introduced it to America in the 17th century.