The 19-year-old, who won gold in the sprint at the Junior World Championships in 2011, raced into the lead after day one in Germany and retained it right up until the final evening.
By then, however, Dohrer (pictured) had pulled level with the Brit at the top and a win, a second and a third-placed finish from the German on the last night gave him the overall victory by a point.
Paul's second place comes a week after Sir Chris Hoy won the General Sprint Masters at Six Days of Rotterdam by a point ahead of team-mate Jason Kenny.
Three events were scheduled for the sixth and final night with Philip Thiele winning the one-lap sprint first up with German team-mate Dohrer second and Paul third.
That left Paul with a one-point deficit, however, victory in the keirin ahead of fellow Brit Callum Skinner and then Dohrer saw him retain the lead going into the last event.
Dohrer was to win the major sprint final, with Thiele in between him and Paul as the German ended with 61 points to 62 from his British rival.
Thiele finished third with 75 points, while Skinner was fifth, three points behind Erik Balzer who totalled 84, and fellow Brit Lewis Oliva was sixth with 96.