In 1964 he returned to the University of Notre Dame as defensive line coach under incoming head coach Parseghian, and held that role throughout Parseghian's 11 seasons, as well as six more (1975–80) under Devine, the last four as defensive coordinator. During that period, he was a part of three Notre Dame national championship staffs (1966, 1973 and 1977) and he coached a dozen All-America defensive linemen. That list included Alan Page, Kevin Hardy, Mike McCoy, Walt Patulski, Mike Kadish, Mike Fanning, Steve Niehaus and Ross Browner—all of whom went on to be selected in the first round of the NFL Draft. Browner won the Lombardi, Outland and Maxwell Awards, and Patulski also won the Lombardi.
On 12 occasions, Yonto′s defensive line ranked among the top 10 teams in the country in terms of rushing defense. Eight of those Irish teams gave up less than 100 rushing yards per game, and the 1974 Notre Dame Fighting Irish ranked first nationally in both rushing defense and total defense (195.2 yards per game). During the Gerry Faust years (1981–85), Yonto served as a special assistant to athletic director Gene Corrigan while handling administrative duties in a wide variety of football areas. Then, he returned to serve as defensive line coach in 1986 and 1987 under Lou Holtz.
Yonto spent three more years as a special assistant to athletic director Dick Rosenthal from 1988 to 1989 through 1990–91. After his retirement, Yonto represented the University and athletics department at a variety of events.