Thomas takes control of Tour of Bavaria after stage win
Britain's Geraint Thomas is pictured on April 4, 2014, in Kortrijk - by David Stockman
The 28-year-old Welshman timed 30mins 48secs over the 25.5 kilometres course round Wasserruedingen, three seconds faster than second-placed Jan Barta of the Czech Republic.
Four-time former world time-trial champion Fabian Cancellara of Switzerland finished a disappointing 13th and nearly a minute off Thomas' pace.
Thomas, who won the 2011 edition of the race, took the yellow jersey off Switzerland's Mathias Frank, who finished sixth on the day and is 19sec adrift.
Sunday's final stage is the 156.6km ride from Wassertruedingen to Nuremberg.