At present it is still unclear what role he will play.
The actress Hayley Atwell (she will be playing Peggy Carter in the film) spilled the beans in a video interview with LeicesterSquareTV.
Some of the rumors have Jones playing the role of General Chester Phillips. Marvel.Wikia.Com describes the character as follows:
Born during the Great Depression, Steve Rogers grew up a frail youth in a poor family. Horrified by the newsreel footage of the Nazis in Europe, Rogers was inspired to enlist in the army. However, because of his frailty and sickness, he was rejected. Overhearing the boy's earnest plea, General Chester Phillips offered Rogers the opportunity to take part in a special experiment... Operation: Rebirth. After weeks of tests, Rogers was at last administered the 'Super-Soldier Serum' and bombarded by 'vita-rays.' Steve Rogers emerged from the treatment with a body as perfect as a body can be and still be human. Rogers was then put through an intensive physical and tactical training program. Three months later, he was given his first assignment as Captain America. Armed with his indestructible shield and and battle savvy, Captain America has continued his war against evil both as a sentinel of liberty and leader of the Avengers.
Captain America: The First Avenger was released July 22nd, 2011 and stars Chris Evans, Hayley Atwell, Sebastian Stan, Tommy Lee Jones, Hugo Weaving, Dominic Cooper, Richard Armitage, Stanley Tucci. The film is directed by Joe Johnston.