1991 Werner began his motorsport career in karting, where he was active until 1997. In 1998 he moved to Formula racing. He took part in the Formula BMW Junior and won the championship in third place behind André Lotterer and Martin Tomczyk. In 1999 he went to the Formula König. After he had achieved in the first season tenth overall, in 2000 he was with 144 to 160 points runner-up behind Bernhard Auinger.
In 2001, Werner in touring car racing and first launched two years in German Ford Puma Cup. After he had reached the fourth place in 2001, succeeded him in 2002 winning the championship. 2003 Werner competed in the German Renault Clio V6 Trophy. He won six of eight races and decided the overall standings for themselves.
2004 Werner received a cockpit with Farnbacher Racing Porsche Supercup, a GT - branded Cup. He stood on the podium five times and finished third in the Drivers' Championship. His teammate Wolf Henzler won the drivers' championship this season. He also took part in this season in a race in the German Seat Leon Supercopa. 2005 Werner had only sporadic racing applications. He graduated four guest appearances in the Porsche Supercup and came in Spa -Francorchamps as the finish line first. In addition, he was also active in the German Porsche Carrera Cup. 2006 won for Werner Farnbacher Racing two races in the German Porsche Carrera Cup and decided the championship with 144 points to 133 against Uwe Alzen for themselves. In addition, he participated in two rounds of the Porsche Supercup.
2007 remained at Werner Farnbacher and drove twofold. For one, he took part in the Le Mans Series and finished eighth in the LMGT2 rating. Secondly, he made his debut for Farnbacher Loles in North America, where he took part in the Rolex Sports Car Series. He won a race in the GT standings and reached in this summary ten podium finishes in 13 starts, so he decided this season for themselves. He was the first non-American to have managed. In addition, he took part in a race in the American Le Mans Series ( ALMS). In 2008 he joined for Farnbacher Loles almost exclusively in North America. He was presented with a summary victory sixth in the GT2 ALMS and eleventh in the GT standings of the Rolex Sports Car Series, in which he remained winless. In addition, he took part in a race in the Le Mans Series. 2009 Werner decided with four runs, the GT- rating of the Rolex Sports Car Series for itself. Together with his teammate Leh Keen, he once again won the league title the GT class. He also took part in the GT2 class at the ALMS. With a podium placement he was 13 In addition, he played for Manthey Racing along with Emmanuel Collard, Wolf Henzler and Richard Lietz in a Porsche 997 GT3 Cup S, the 24-hour race on the Nürburgring and reached number three. He also took part in some of Mamerow Racing race of the BFGoodrich Endurance Championship and won with Christian Mamerow the last three races in a row.
2010 Werner works driver was at BMW. He went to no full season. He competed in the Le Mans Series, ALMS and debuted at the 24 Hours of Le Mans. He completed this race with Dirk Müller and Andy Priaulx. In the GT2 class of the ALMS, he scored a podium placement. In 2011, Werner participate in the full season of ALMS. Together with his teammate Bill Auberlen he stood in five of nine races on the podium of the GT standings and was the end of the season along with Auberlen third in this category. In addition, he started once again in a race of the Le Mans Series and took along the 24-hour race at Le Mans in part with Augusto Farfus and Dirk Müller. He also fell in 2011 in a race of the Blancpain Endurance Series at the start and went in 2010 and 2011 at the 24-hour race on the Nürburgring.
2012 Werner received a BMW cockpit at Schnitzer in the DTM. In the race at the Norisring, he scored his first point in tenth. With a fourth place as best result he finished ninth in the drivers' standings, while his team- mate Bruno Spengler DTM Champion. In addition, he took in 2012 in a race the Rolex Sports Car Series in part. 2013 Werner remained the BMW DTM Team Schnitzer. Already the season opener at Hockenheim, he scored his first podium placement with a second place. At the end of the season, he finished 13th overall.
- 2006: German Porsche Carrera Cup (Master)
- 2006: Porsche Supercup ( No. 20 )
- 2007: Rolex Sports Car Series GT (Master)
- 2007: Le Mans Series, LMGT2 (8th place )
- 2007: ALMS, GT2 ( 25th place )
- 2008: Rolex Sports Car Series GT (11th )
- 2008: ALMS, GT2 ( 6th place)
- 2008: Le Mans Series, LMGT2
- 2009: Rolex Sports Car Series GT (Master)
- 2009: ALMS, GT2 ( 13th)
- 2010: ALMS, GT2 (11th )
- 2010: Le Mans Series, LMGT2 ( 14th)
- 2011: ALMS, GT ( 3rd place)
- 2011: Le Mans Series, LMGTE Pro
- 2011: Blancpain Endurance Series, GT3 Pro ( 14th)
- 2012: DTM ( 9th place)
- 2012: Rolex Sports Car Series GT
- 2013: DTM ( 13th place)