Born in Dortmund, he was the eighth driver to complete the informal triple crown in endurance racing.

Werner was a regular driver in the STW and Porsche Supercup during the 1990s, but he found more success in the 24 Hours of Daytona, which he won in 1995 in a Kremer-Porsche.

In 2001 he joined Audi Sport Team Joest, becoming a regular driver in the American Le Mans Series.

In 2008, he co-drove the Audi R10 in the American Le Mans Series with Lucas Luhr to six overall victories and eight class wins, taking the LMP1 drivers title.

After his last 24 Hours of Le Mans participation in 2010, Werner became a regular participant in historic racing, winning the 2022 Historic Grand Prix of Monaco Série G race(for 3-litre Formula One cars from 1981 to 1985), in a Lotus 87B.