When you create the junction table, set the Is Primary Key property of both columns to True. This way, you create a composite key which in turn means each combination can only exist once.
Next, for this table, click New and create a new Relationship between the Foreign Key Table (the junction table) and the first Primary Key table. In your case, link PKtable1id to the ID of Table1. Then repeat this for the second table and link PKtable2id to the primary key of Table2.
This way, the individual columns of the composite key each refer to their respective related table.
Hope this helps,