A judge on Friday suspended the original court ruling that imposed the fingerprinting of US travellers but he left the final decision up to the federal government.
And on Saturday the foreign ministry said it would keep the system in place in Rio and the rest of Brazil for at least 30 days.
Rio had filed the appeal, saying the fingerprinting would harm tourism. US tourists spend about $250 million in Rio each year.
At Rio's international airport and at the sea port, US tourists were again waiting on Monday in the long queues that have become common since the system went into effect on 1 January in response to the similarly controversial scheme in the US.
"It is very frustrating to come to Brazil and spend 45 minutes in the line after long hours on the plane."
The United States on 5 January started fingerprinting and photographing visitors, including Brazilians, who need visas to enter the country as part of anti-terrorism controls.
The system exempts citizens of 27 mainly European nations who do not need visas for short trips.
In retaliation, a Brazilian judge ordered the fingerprinting of US visitors.
"It is very frustrating to come to Brazil and spend 45 minutes in the line after long hours on the plane," said Olivia Doerhe, a 20-year-old student from Iowa. She said it took the officials 10 minutes to take her fingerprints and photographs.
Some complained they had been stranded in queues while federal police officials were lunching. But airport officials said the time visitors spent waiting was now much shorter.
Brazilian President Luiz Inacio Lula da Silva and US President George Bush, in Mexico for the two-day Americas summit, were set to discuss the measure, which has been hailed by many Brazilians but labelled discriminatory by Washington.
Rio mayor's office said the measure had led to cancellations of group tours and damaged the city's economy.
To soften the blow, Rio tourism authorities have taken steps to make Americans feel welcome.
Starting on Tuesday US tourists will be greeted with T-shirts saying "Rio loves you" and given souvenirs and flowers as compensation for their discomfort at the airport.