The former Mainz coach was appointed by the Thessaly club on December 16 but failed to halt the tide of defeats which have left the club rooted to the bottom of the 16-team table with just 11 points from 17 matches.
Larissa went down to a 1-0 defeat at Kavala on Saturday, their 10th loss of the campaign.
A club spokesman said that former AEK Athens and Asteras Tripolis coach Kostenoglou had been appointed on a six-month contract until the end of the season.
Kostenoglou, 40, is the club's third coach of the campaign after Marios Ouzonidis and Anderson.
Larissa, who moved into an impressive 16,000-capacity stadium in December, are in danger of relegation.
Last week more than 500 fans smashed the windows of Larissa's team coach after pelting it with rocks, eggs and yogurt after the team returned from Athens following a 3-0 defeat by Atromitos.
Players and staff were shocked after they were left stranded inside the vehicle for four hours as angry fans set up a blockade by lighting bonfires in front and behind the bus so it could not move.
Olympiakos preserved their five-point lead at the top of the standings with a 2-0 away victory at Kerkyra on Sunday.
A headed own goal by Kerkyra defender Thanasis Tsigas from Ariel Ibagaza's free-kick put the Reds ahead before Belgian forward Kevin Mirallas notched his ninth goal of the season for Ernesto Valverde's side in the 70th minute to seal the points.
Panathinaikos maintained the pressure on Olympiakos with a 1-0 win over Aris behind closed doors at the Olympic stadium On Saturday.
The match was the second and final game in an empty stadium as punishment for a December 18 pitch invasion when fans chased the players off the pitch and pelted them with missiles after a surprise home defeat.
Sotiris Ninis's 19th-minute volley ensured the Greens stayed in second place on 37 points, five points behind Olympiakos.
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