Only 195 votes were cast, below the threshold of 200 needed for the vote to count.
"The entire nation is watching the decision being made here at the National Assembly today. World is watching," National Assembly speaker Woo Won-shik said with a sigh. "It's very unfortunate that there wasn't even a vote."
The main opposition Democratic Party has said it will revive the impeachment motion next week if it failed on Saturday.
Yoon shocked the nation late on Tuesday when he gave the military sweeping emergency powers in order to root out what he called "anti-state forces" and overcome obstructionist political opponents. He later rescinded the order.
He apologised to the nation in a speech on Saturday morning but resisted calls to resign ahead of the vote.
