She punched her fists in delight on crossing the line.
The German crew of Fischer, Maike Nollen, Katrin Wagner and Carolin Leonhardt finished less than a metre ahead of Hungary while Ukraine took the bronze medal.
Fischer, 42, won her first Olympic gold as an 18-year-old in Moscow in 1980 and has not ruled out competing in Beijing in 2008.
Hungary, roared on by their boisterous supporters, have been world champions since 1999 and also won silver at the Sydney Games in 2000.
It was not the same story for Germany in the men's C1 1,000, where Spain's David Cal stunned the defending Olympic champion Andreas Dittmer to win by half a second.
Dittmer had been tipped for gold again after winning 13 world cup races and the last three world championship titles.
Cal, silver medallist at the 2003 world championships, had a steady start but ground out a lead of just under a length by 500 and Dittmer was unable to catch him.
He held on to take gold over Dittmer while Hungary's Attila Vajda finished third to the delight of the flag-waving Hungarian fans.
In the first race of the day, Norway's Eirik Veraas Larsen came from behind to win the men's K1 1000 Olympic gold by clear water.
Larsen came to the Games as one of the favourites after winning two world cups this season and had looked dominant throughout the Olympic regatta.
Canada's Adam van Koeverden was the first out of the blocks but was slowly reeled in by Larsen in the second half of the race.
New Zealand's world champion Ben Fouhy came through on the line to win silver and van Koeverden took bronze.