The Chamber of Deputies, which is dominated by his governing Colorado Party, voted 42 to 36 to reject impeachment.
Outside, hundreds of protesters threw stones at police who responded with water cannons and rubber bullets. Some protesters smashed store windows and car windshields, while shouting anti-Abdo slogans. Several people were arrested.
Recent days have seen a series of protests against Abdo’s government amid overwhelmed hospitals and shortages of vaccines and drugs for COVID-19 patients. The shortages prompted Wednesday's bid by the opposition to remove him from office.
Some doctors and nurses have joined the protests.
“It was time for Abdo Benítez and his entire government to leave office because they did nothing to confront the coronavirus. There are no vaccines, there are no drugs in hospitals, and the hospital infrastructure is deficient,” Kattya González, a legislator with opposition group Encuentro Nacional, said at a news conference.
More than 183,000 confirmed coronavirus cases and 3,554 deaths related to COIVD-19 have been registered in the South American country of 7.6 million people.
Opposition lawmakers emphasized, among other things, that so far only 24,000 vaccine doses have arrived in Paraguay.