The club announced on Tuesday that they had parted company with Nathan Arnold by mutual consent.
The Owls are currently ninth in the NPL East Division, 10 points outside the play-off places with six games remaining.
The duo’s first game in charge will be on Saturday, when Cleethorpes welcome Brighouse Town.
On taking the job, Lowe said: “I feel very proud to have the opportunity to lead alongside Dicko this fantastic club until the end of the season.
“I have been at Cleethorpes Town for over 10 years now and the club has a big place in my heart.”
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