After F1, Fontana raced in Formula 3000, and he also made 8 CART starts in 2000 with a best finish of 11th at Cleveland. He subsequently moved into TC 2000, a national touring car racing series, in his native Argentina.
In 2006, in the Argentinian Magazine Olé, Fontana claimed that Jean Todt visited the Sauber motorhome during the weekend, and told Peter Sauber that the Saubers must block if they were in a position to do so in order to help Michael Schumacher win the World Championship. This was subsequently denied by both Sauber and Todt. Peter Sauber told Swiss newspaper Blick: "In the nine years that we co-operated, Ferrari never expressed the desire that we should obstruct an opponent of Schumacher's on the track."