The Thessaly club are the only team outside of Athens and Salonika to win the Greek title - a feat they achieved in 1988.
"The team was completely demoralised when I came. We had an opportunity to try to reverse the situation but it was not possible. In some matches we played well and I believe we did not lose any matches easily," said coach Nikos Kostenoglou who took charge in early January.
Despite opening an impressive 16,000-capacity stadium in December, Larissa struggled with poor form throughout the season and made three coaching changes.
Asteras Tripolis were also relegated on Sunday after a 1-0 defeat at second-placed Panathinaikos.
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