Duke and USC
Jones coached in 1924 at Trinity College, now known as Duke University, before leaving for USC in 1925. In 16 seasons at USC, Jones coached seven Pacific Coast Conference championship teams and four more national champions, and won each of the five Rose Bowls in which his Trojans played . In the 1920s, USC won two Rose Bowls, in 1923 and 1930. Heading into the 1930 Rose Bowl, USC had defeated its crosstown rival UCLA 76–0 in their first meeting.
Moments before a USC-Stanford game, Jones visited the Stanford locker room and discovered Stanford All-American halfback Bobby Grayson was nursing an injured knee. Jones returned to the USC quarters and instructed his players to avoid hitting Grayson in the crippled leg. They never did.
In 1939 and 1940, Jones's teams again won the Rose Bowl. In those two Rose Bowl games, USC faced teams that were unbeaten, untied and unscored-upon. First it was Duke, which led after an early fourth quarter 23-yard field goal by Tony Ruffa, but backup USC quarterback Doyle Nave completed four straight passes to "Antelope" Al Krueger who outmaneuvered Eric "The Red" Tipton, scoring the winning touchdown with one minute remaining. Krueger's touchdown marked the first points scored against Duke during the season. In the 1940 Rose Bowl, the Trojans defeated the Tennessee Volunteers 14–0, ending a 23-game Tennessee winning streak and scoring the first points scored against the Volunteers all season.
USC historian Al Wesson remarked, "Howard lived and breathed football. If it were not for football, he would have starved to death – couldn't possibly have made a living in business."
One of the players Jones coached while at USC was legendary film star John Wayne.
Wesson also recalled, "His assistants tried to get him to organize the practices and let them do most of the heavy work. He'd promise to do it, but after 15 minutes on the field, he'd be down on the ground showing them personally how to block, following every play on the dead run, and acting as though he were still playing end at Yale. He just couldn't relax and let others do the heavy work."
Jones lived in Toluca Lake, California. On the hot morning of July 27, 1941, while home alone and washing and waxing his car, Jones fell ill and called his doctor, who lived nearby. By the time he arrived, Jones was dead; he had suffered a heart attack. The sudden, unexpected death was a shock to family, friends and fans: Several thousand people attended his funeral at First Methodist Church in Hollywood. He was buried in Woodside Cemetery & Arboretum at Middletown, Ohio.