Williams began racing in the early 1960s in saloons and junior formulae before graduating to Formula Three in 1963. By 1966 he was driving for the de Sanctis team. During these formative years he worked alongside Frank Williams (no relation), Sheridan Thynne, and Piers Courage, forming part of a close circle of young British drivers making their way through European junior categories. In 1964 he briefly toured the European Formula Three circuit with Courage in Lotus 22 machinery.
In 1967, Jonathan Williams was signed by Scuderia Ferrari, initially as a sports car driver. The season was a turbulent one for the team: Lorenzo Bandini, the team leader, died from injuries sustained at the Monaco Grand Prix, and Williams's sports car co-driver Günter Klass was killed during practice at Mugello in July. Despite these losses, the team offered Williams an opportunity in Formula One later in the year.
His sole Formula One World Championship start came on 22 October 1967 at the Mexican Grand Prix. He finished eighth, outside the points under the scoring system then in use. Ferrari dropped him from the programme after that single race, and a subsequent Formula One project with Abarth did not progress.
Williams returned to Formula Two competition in 1968, winning the Rhine Cup race in a car entered by Frank Williams. He also drove the works Serenissima. In 1969, he played a practical development role for Frank Williams Racing Cars, helping develop the De Tomaso Formula One car that Piers Courage would drive in the 1970 season, while continuing to race in Formula Two himself.
Williams's most visible contribution outside the cockpit came at the 1970 24 Hours of Le Mans, where he co-drove a Porsche 908/02 that carried cameras for Steve McQueen's racing film Le Mans. The car's role in capturing footage for the production made Williams a minor figure in cinema history as well as motorsport. He retired from racing in 1972 and subsequently became a pilot, initially working for Alessandro de Tomaso in that capacity, a role he later described as one he disliked. He then worked as a writer and photographer.
Williams died on 31 August 2014, aged 71. He appeared posthumously in the documentary Steve McQueen: The Man and Le Mans, which was released nine months after his death and closes with footage of Williams driving during the 1971 film.
Jonathan Williams occupied a characteristic position in 1960s British motorsport: a capable driver whose single Formula One appearance did not reflect the breadth of his competitive experience across multiple categories. His early association with Frank Williams and Piers Courage placed him at the centre of the amateur-to-professional transition that many young British racers navigated through European Formula Three in the mid-1960s, and his later technical involvement with the De Tomaso F1 project gave him a role in one of the more unusual privateer programmes of the era.