The world champions had looked untouchable in the early part of the season as they claimed victories in the first five events.
But they were absent from the top step of the podium in the previous two rounds, with compatriots Toni Eggert and Sascha Benecken closing the gap in second.
However Wendl and Arlt recovered in Lake Placid, recording a time of 1:28.256 minutes over their two runs to take the win and with it win back the overall World Cup title they last held in 2011, after having to settle for silver last year behind Andreas and Wolfgang Linger.
And the Germans did it in style as they recorded a new start record of 6.202 seconds en route to their sixth win of the season.
Eggert and Benecken could only manage seventh in America to hand Wendl and Arlt the title, and now face a fight with Austrians Peter Penz and Georg Fischler to finish runner up after the latter were second in Lake Placid.
Eggert and Benecken have 598 points while Penz and Fischler are 73 behind with just one more round to come.