On 17 February 2006 he won the Winter Olympics silver medal for the 15 km cross-country classical.

In season 2007–08 he was overall winner of the men's version of the Tour de Ski and FIS Cross-Country World Cup.

In 2010, he again won the Tour de Ski in a dramatic come-from-behind victory over Norwegian skier Petter Northug.

Bauer finished with the bronze medal in the 15 km freestyle event at the 2010 Winter Olympics.

After a career in which he collected three Olympic and two World Championship medals, Bauer confirmed his retirement from competing for the Czech national team after the 2017 Nordic World Championships in Lahti, although he indicated that he would continue competing in long-distance races for his own team, which he had set up three years previously.