"You came here today to seek the progress of a royal pardon from a government that is afraid of my return," he said.
"We will fight peacefully. We have to be peaceful so that his majesty will recover soon."
Thaksin did not mention his location, but red shirts on stage claimed he was calling from Papua New Guinea.
Call for clemency
The red shirts, organised by the United Front for Democracy Against Dictatorship (UDD), believe Thaksin is a victim of a vendetta by opponents in the military and the Thai establishment.
They say these elements plotted the coup that toppled him and ensured he was convicted of corruption to keep him sidelined.
Jatuporn Prompan, one of the leaders at Saturday's protest, said the government was dragging its feet over the petition to pardon Thaksin.
"We are here to send a signal to the government... We will come back by the end of the month. The protest will not end quickly," he said.
The UDD handed its petition to the government in mid-August.
But Abhisit Vejjajiva, Thailand's prime minister, has said that it will take at least two months to process the petition, which Thaksin's supporters hope would prompt his return and a political comeback.
Analysts say that would potentially deepen rifts and further destabilise what is Southeast Asia's second-biggest economy.
King Bhumibol's illness has already shaken the Thai stock market, as the monarch is considered the only unifying figure in a politically fragile nation.