Very simple, open up the worldbuilder save file in notepad. First there will be a section detailing game options; next, a section detailing team info; next, a section detailing players; then a section detailing map statistics and finally a section where each plot is described.
In the second section, the team info, contact is described. For Team 0 it will say ContactWithTeam=0 if it doesn't have contact with anyone. If it has contact with team 1 (that is, the second player) it will say ContactWithTeam=0,1. Etc. Just change it to no contact by making sure all teams have contact only with their own team number.
Obviously you will first have to move the two players' units out of sight of each other before you do this, or they will simply make contact again the moment you reopen the map in the game.