Kerala Governor Justice (retd) P Sathasivam administered the oath of office to Thomas at the Raj Bhavan.
Chief Minister Pinarayi Vijayan and his cabinet colleagues were present at the function.
Thomas is likely to be assigned the Transport portfolio.
A three-time MLA from Kuttanad in Alapuzha district, he is the fourth minister from the district.
NCP's Saseendran had resigned on March 26 after a purported audio clip of him speaking in sexual undertones to a woman was aired by Malayalam channel Mangalam.
NCP leaders and Thomas Chandy's relatives were among those present at the swearing-in ceremony.
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