Guoga showed up in person for the meeting to read out his statement that he was resigning "of his own free will".
The commission's decision will take effect on Saturday.
In January, the election watchdog did not grant Guoga's request to cancel his mandate because he failed to attend its meeting in person, as required by law.
Googa submitted his request to the commission on January 12, asking it to cancel his mandate as of January 14. The MP, who ran for parliament with the Lithuanian Labor Party, said he was resigning because he saw no possibilities to deliver on his election promises.
Guoga will be replaced in the Seimas by Skardzius, the next-in-line candidate on the opposition Labor Party's list in last autumn's parliamentary election.