On June 8, 2005, the Tigers traded Urbina along with infielder Ramón Martínez to the Philadelphia Phillies in exchange for second baseman Plácido Polanco.
He made his last Major League appearance on October 2, 2005, during a 9–3 Phillies victory over the Washington Nationals at RFK Stadium.
On November 7, 2005, Urbina was arrested in Venezuela on a charge of attempted murder for an incident that occurred on October 16. Urbina attacked five farm workers on his property whom he had accused of stealing a gun, wielding a machete and attempting to pour gasoline on them. On March 28, 2007, Urbina was convicted of attempted murder and sentenced to fourteen years and seven months in prison. He was released on December 24, 2012, after serving just over seven years of his sentence.