Beginning in 1987, Vavra coached in the Dodgers' minor league system. While at Yakima, Washington in Class A, he was named Manager of the Year for 1994 and 1996 for the Northwest League after winning the division title in 1994 and the League championship in 1996. Vavra coached for ten years in the minors before moving to the Dodgers' major league staff. He served in special assignments and as a roving coach before becoming the permanent bunting and baserunning coach in 2000.