After retiring from the Court, he went into politics becoming a Senator of Colombia in 2002, and running for President as an Alternative Democratic Pole candidate in the 2006 presidential election, ultimately losing to ex-president Álvaro Uribe Vélez, who was seeking his second term in office.

[11] He ran for the presidency of Colombia for the 2006–2010 term, as the candidate of the Alternative Democratic Pole, after winning the bloc nomination over Antonio Navarro.

One of his main political proposals was to attempt to change Colombia's socio-economic model, which he believed to exemplify some of the worst characteristics of capitalism at a global and local level.

Gaviria argued, as do many of his supporters, that this gap has increased over the 2000s and continues to grow, in part due to the economic policies of President Álvaro Uribe's administrations.

Gaviria was also a strong defender of Colombia's 1991 Constitution, in principle, but believed it necessary to fully apply its chapters on human, ethnic and political rights, while at the same time restoring some of the controls that he considered the government and the state should have over the nation's economy and society.