The musician had called the cover – which was performed by Darren Criss and Matt Bomer – "dinky and wrong... like it's playing to you from a cardboard box".
However, according to The Hollywood Reporter, Gotye explained his remarks during a private performance in Los Angeles yesterday.
He complimented the show's version of his song, saying: "I thought it was really clever to transpose the song to two guys... It was a great idea.
"The nature of using reverb and space in a recording can change your perception of how a sound appeals to you."
He went on to say that he had made his comments in reference to "this xylophone hook in my song - it's kind of dinky not just in the cover version but the original song.
"Somehow, that becomes 'the Glee cover I hated and Darren Criss is an asshole'."
Gotye performed the song during his recent television debut on SNL.
Watch Darren Criss and Matt Bomer perform 'Somebody That I Used To Know' on Glee below: