Zubkov and Arndt are currently locked in a fierce rivalry for overall honours on the World Cup circuit this season with just 47 points separating the German in first from the Russian with one round to go.
And they ensured the challenge was transferred over to the World Championships in Switzerland as defending World Cup champion Arndt led Zubkov by 0.05 seconds after the first run.
However Zubkov turned the tide in run two for an advantage of 0.05s over Arndt himself at the halfway stage with the final two outings scheduled for Sunday in St Moritz.
Arndt clocked 1:05.21 and 1:05.68 while Zubkov posted 1:05.26 and 1:05.58 for the lead with defending world champion Steven Holcomb occupying third place.
Holcomb holds a 0.01s advantage over Switzerland's Beat Hefti in fourth while Francesco Friedrich, who won the two-man world title in St Moritz last weekend, is fifth, 0.10s further adrift.
Another German Manuel Machata is sixth with Thomas Florschuetz seventh, 0.44 and 0.45 behind overall respectively, before British No.1 pilot John Jackson in eighth.
Jackson and his crew of Stuart Benson, Bruce Tasker and Joel Fearon were 13th after posting 1:05.84 on their first run however vast improvements saw them move up the field.
They clocked 1:05.46 second time out and are just 0.16 away from Holcomb in bronze-medal position while British No.2 pilot Lamin Deen is currently ranked 23rd, 2.28 behind overall.