Skill trials of ninjas that increase the cd of the target.

P.S. You may beat in arena the common meta with shisui and bee sst by running kurama + kushina habanero + kisame samehada/madara 5ks and wind/water main relatively easily as far as you own initiative.

Outside arena you just flat out nuke his supporters and let him die by multiple attacks per round in round 3+.

If you own kakashi susano'o you can just run shark bomb team (if you are faster).

Otherwise your best bet, since is autoteam, is to run blitz teams where you make sure that your key ninjas are not targeted directly by naruto's chase.

Hokage minato + earth main is a good duo to deal with it, for example.

Another counter is edo tobirama (both if directly interrupts him and if he is able to interrupt him thanks to his chase (example kurama as a combo trigger).