The cross was atop the historic San Gabriel Mission depicted on the seal before it was removed under threat of legal action by the ACLU of Southern California during a redesign of the seal in 2004.
The mission at the time was undergoing earthquake retrofitting and did not have the cross on top. The cross was reattached to the building in 2009.
Supervisors Michael Antonovich and Don Knabe filed a motion to add the cross to the seal for historical accuracy.
"What we have is correcting a situation where the mission has the cross because it is historical. We are not adding, we are just reflecting upon a historical event," said Antonovich.
"In a county as pluralistic as this, with as many different religious beliefs, there is no basis for the county to be adding that symbol when so many other faiths will be completely left out," said Peter Eliasberg, legal director of the ACLU of Southern California.
The Associated Press contributed to this report.