Only 25 lawmakers voted in favor of the motion to strip Morales of his immunity, far fewer than the 105 needed in the 158-member legislature.
Morales is under investigation by the UN International Committee Against Impunity in Guatemala (CICIG) and Guatemalan prosecutors for allegedly failing to declare $1 million in campaign funding to his party in 2015, the year he was elected to office.
He sparked a storm on August 27 by ordering CICIG chief Ivan Velasquez out of the country, two days after the Colombian applied to have Morales's immunity lifted.
But Guatemala's top court overruled the order and the CICIG is forging on with its probe.
The CICIG is widely respected in Guatemala.
It helped Guatemalan prosecutors investigate a corruption scandal that toppled the previous president, Otto Perez, in 2015, paving the way for the election of Morales, a former TV comic with no previous political experience who campaigned on anti-corruption promises.
A congressional committee on Sunday had recommended that the president's immunity be lifted.
But analysts said ahead of the vote that outcome looked unlikely because of the party alliances of his conservative National Convergence Front.
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