The 57-year-old, who coached the Piraeus club from 2000-2002 and again from 2006-2008, replaces the sacked Portuguese Paulo Bento, who departed earlier this month after a poor string of results.
Interim coach Vasilis Vouzas, who has been handling senior team affairs since Bento's departure, will return to his role as Under-20 coach.
"Mr. Lemonis is part of the history of our club, he has served Olympiacos as a player and a coach winning titles and trophies along the way," the club said in a statement.
Olympiacos had held a 13-point lead in the title race until a recent dip in form saw them lose three successive domestic league matches for the first time in 21 years, which culminated in Bento losing his job.
The Red and Whites then suffered a humiliating Europa League Round of 16 exit in a 5-2 aggregate defeat to Turkish side Besiktas, followed by a 1-0 loss to arch-rivals Panathinaikos in the Athens Derby last weekend – a result which saw their lead cut to just six points with five matches to play.
"I am very happy to be back at this club. I am even more prepared and more experienced, to help the team pursue its goals, which is of course winning the championship and the Greek Cup," Lemonis, also a former player at the club, said.
"Everybody knows I am Olympiacos through and through, but now it is time for hard work, not words.
"We want our fans closer to us than ever, since we are always the team leading the way and the one everybody wants to see fall. We will make our statements on the pitch."
Lemonis now has a week to settle in and get his team ready for their next league match after the international break, which is a home match against playoff-chasing Platanias on April 1.
(Reporting by Graham Wood, editing by Sudipto Ganguly)
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