In late 1997, Audi introduced an all-new range of Audi A6 models, based on the Volkswagen Group C5 platform. A new Audi S6, now officially known as the Audi S6 quattro appeared in 1999, to complement its A6 platform-mate. It was available in a four-door saloon/sedan and a five-door Avant (estate/wagon). In North America, the Avant bodystyle was the only version available. The vehicle could accelerate from standstill to 100 kilometres per hour (62.1 mph) in 5.7 seconds, and from 0 to 200 km/h (124.3 mph) in just 21.7 seconds. The top speed was electronically governed to 250 km/h (155.3 mph).

This generation of S6 went out of production in 2003.