In 1960, he joined the Boston Patriots of the new American Football League as an assistant under head coach Lou Saban, coaching the offensive backfield. Holovak took over as head coach for the final nine games in 1961 after Saban was fired after a 2–3 start, and remained as head coach through 1968. In 1976, he served one game as head coach for the New York Jets. He was also the general manager of the Houston Oilers from 1989 to 1993. Holovak was inducted into the College Football Hall of Fame as a player in 1985.