Bayley, 27, and Shilton, 16, defeated Jordi Morales and Alvaro Valera 3-1 in the men's class 7 final in Lasko.
Fellow Briton Megan Shackleton, 16, and Slovakian playing partner Alena Kanova took silver in the women's class 4 team event, after losing to Serbia 3-2.
Jane Campbell and Sara Head won women's class 3 team bronze for Britain.
Will Bayley and Billy Shilton won Para table tennis team gold for Britain at the Slovenia Open by beating world champions Spain.