Kowalczyk is bidding to win her fourth straight Tour de Ski title over the next week and started by finishing third in the opening prologue stage on Saturday.
That meant she began the 9km classic pursuit in Germany 5.3 seconds behind 2008 Tour de Ski winner Charlotte Kalla and 14.7 shy of Kikkan Randall.
Randall won the opening stage to take the early lead with Kalla second, however there was to be no denying Kowalczyk victory second time out in Oberhof.
Kowalczyk bridged the gap between herself and Kalla not soon after the start before overtaking Randall seven minutes into the 9km classic pursuit.
The Polish cross-country skier then broke away building a lead of over 30 seconds by the last and final lap to win in a time of 25:01.4 minutes.
Kowalczyk’s winning margin was 41.4 seconds by the finish with Norway’s Therese Johaug taking second 3.6 ahead of Finland’s Anne Kylloenen in third.
Johaug’s performance was impressive in the absence of Norwegian team-mate Marit Bjoergen as she made up a deficit of 32.2 seconds to finish second.
She finished 13th in the 3km freestyle prologue but stormed to second in the pursuit while Kalla was 11th and American Randall was 14th.
With the bonus seconds applied for finishing first, Kowalczyk now leads the Tour de Ski after two stages by 46.4 seconds ahead of Johaug.
Kowalczyk and the rest of the field now have a rest day before the sprint in Switzerland something she is vowing to make the most of.
“It feels great to win but I am so tired. The conditions were hard and the race was hard but it is amazing to have won,” said Kowalczyk.
“My skis were working perfectly, they were fast and I was really good uphill.
We now travel to Switzerland and I may look at the track and do some skiing but not too much.”