The pair were among two groups in the canyon who were surprised on Sunday afternoon by rising waters triggered by heavy rainfall, cantonal police said.
One group managed to escape the torrent without injury.
Three members of the other group were taken to hospital for treatment of minor injuries after being rescued by a Rega search and rescue team.
But the other two members of the group were carried away by the current of the river, which empties into the Walensee, a lake that straddles the borders of the cantons of Saint Gallen and Glarus.
A search for the pair ensued, involving 60 people from the Swiss Alpine Club (SAC), search and rescue experts, the local fire department and cantonal police.
A helicopter initially pressed into service was eventually grounded because of poor weather.
SAC members finally pulled the bodies of the two missing members from the river at around 11pm, police said.
The exact circumstances of their death remain under investigation.
Canyoning can be a high-risk sport, as this YouTube video of aficionados in the Fallenbach River illustrates.
Among other things, it shows people, equipped with helmets and special gear, rappelling down waterfalls and jumping from steep cliffs into pools in the river.
The sport involves navigating through canyons, using a variety of techniques such as scrambling, climbing, abseiling and swimming.
Flash floods are among the biggest dangers to those practising canyoning.
In a widely publicized Swiss accident, 18 tourists and three guides died in 1999 while canyoning in the Saxetenbach Gorge in the canton of Bern.
Six people at the head of the group organizing the trip, Adventure World, were later found guilty of homicide by negligence by an Interlaken court.
They received suspended jail terms and fines ranging from 4,000 to 7,500 francs.