The Syco boss made the comments following Aliki Chrysochou's performance during the June 1 semi-final.
"What's interesting is, with Katherine Jenkins taking a big dip at the moment, maybe your time has come," he said.
Cowell has since taken to Twitter to apologise publicly, as well as reaching out to the classical star privately.
Sorry Katherine. X— Simon Cowell (@SimonCowell) June 2, 2013
Jenkins recently left her label Warner Music, teasing that she is "sworn to secrecy" about where she is going next.
She also played down reports that Warner had decided against renewing her contract after she had lost the company an estimated seven-figure sum.
Watch Jenkins perform 'Hallelujah' below: