The ruling by Judge Ricardo Mucio Santana de Abreu Lima came just hours after another judge upheld an earlier judicial order suspending WhatsApp's services. The application was working again by Tuesday afternoon.
The suspension had gone into effect Monday shortly after it was ordered by Judge Marcel Maia Montalvao, in the northeastern state of Sergipe.
A court official in Sergipe said the suspension was ordered because WhatsApp has repeatedly failed to turn over information about its users for an investigation into drug trafficking and organized crime.
WhatsApp officials have estimated that the service is used by 100 million Brazilians.
"Yet again millions of innocent Brazilians are being punished because a court wants WhatsApp to turn over information we repeatedly said we don't have," the messaging service's CEO and co-founder Jan Koum said on his Facebook page after Montalvao's ruling. "We encrypt messages end-to-end on WhatsApp to keep people's information safe and secure, we also don't keep your chat history on our servers."
"We have no intention of compromising the security of our billion users around the world," he added.
Montalvao's suspension was the latest chapter in a dispute between Brazilian law enforcement and Facebook, which bought WhatsApp in 2014.
Calls to Facebook's offices in Sao Paulo went unanswered on Tuesday.
In March, Facebook's most senior representative in Latin America was detained in Sao Paulo and held overnight.
At the time, a spokeswoman for federal police in Sergipe, Monica Horta, said investigators had requested content from a WhatsApp messaging group as well as other data, including geolocation. Investigators first contacted WhatsApp several months earlier but hadn't received a response, Horta said.
Brazilian authorities also clashed with Facebook in December, when a judicial order forced telecoms to block WhatsApp for about 12 hours over its alleged refusal to cooperate with a police inquiry.
Facebook CEO Mark Zuckerberg at the time said he was "stunned" by the "extreme decision.
Get your daily dose of tech news, reviews, and insights, in under 80 characters on Gadgets 360 Turbo. Connect with fellow tech lovers on our Forum. Follow us on X, Facebook, WhatsApp, Threads and Google News for instant updates. Catch all the action on our YouTube channel.