Lee Joon-Seok, on trial for murder in the city of Gwangju, was vilified after the April disaster for abandoning the stricken ferry while hundreds were still trapped inside.
More than 300 people perished, most of them school children in a tragedy that stunned South Korea.
The captain and many crew members were among the first to climb onto rescue boats.
Video footage taken from the phones of those who perished showed increasingly worried students patiently waiting in their bunks as messages were broadcast over the ship's tannoy telling them to stay where they were despite the ferry listing heavily.
"I sincerely apologise to the victims and their relatives and I will pray for them for the rest of my life", Lee said at his trial, according to Yonhap news agency.
"I think I deserve a death penalty for what I have done. But I never thought for a moment to sacrifice the passengers (to save my own life)".
"No matter how God helps me, I know I won't be able to leave the prison before I die. But I cannot give my children and grandchildren a bad name as a murderer's relatives", Lee added.
The message was never relayed, he added. But Lee he was unable to provide any evidence that he issued this instruction.
The disaster caused outrage in South Korea, knocking the entire country off its stride and triggering widespread public anger as it emerged that incompetence, corruption and greed had all contributed to the tragedy.
Lee has insisted that the ferry owners are the real culprits of the disaster as it was their decision to consistently overload the vessel and commission an illegal redesign.
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