Three-time world champions Eggert and Benecken were quickest in the final race to seal their triumph.
Wendl and Arlt, who won Olympic gold medals in 2014 and 2018, were second fastest in the final race and end as overall runners-up.
Latvian pair Andris Sics and Yuri Sics finished third in Konigssee and the overall standings.
Eggert and Benecken's victory gives them a final tally of 872 points, ahead of Wendel and Arlt on 847 and the Sics pair on 720.
Eggert said: "It has been an incredibly exciting season. There have been winter seasons where we've had a big points cushion going into the last round.
"Our rivals have become stronger. We had to prove our nerve a couple of times this season – at the World Championships in Sochi and here at the season finale."
Wendl paid credit to the victors and said: "Toni and Sascha were just better today.
"We need to analyse where we can improve. One thing is clear – not our starts!"
Andris Sics added: "It has been a good season. We could have done better at the World Championships. We are like wine – we get better with age."