Homeland star had told The Guardian that he didn't want to end up a "fruity actor... playing wizards" later in his career, which was interpreted as a reference to McKellen or to Michael Gambon.
And McKellen - who plays Gandalf on the big screen - responded in the Radio Times.
"I wouldn't like to have been one of those actors who hit stardom quite early on and expected it to continue and was stuck doing scripts that I didn't particularly like just to keep the income up.
"I've always wanted to get better as an actor. And I have got better. You've only got to see my early work to see that.
"As for a fruity voice? Well, it may be a voice that is trained like an opera singer's voice: to fill a large space."
He also appeared to link Lewis' use of the term "fruity" with wariness among gay people about coming out.
"It's true of A-lists all over the world—A-list priests, A-list politicians. What will people think? Will people still vote for me? Will people come see me act?
"They're warned by the people who surround them, agents and managers who have a living to make and are worried that the actor will get pigeonholed.
"I don't think the audience gives a damn…You don't have to be straight to play Gandalf. Anyway, who says that Gandalf isn't gay? I loved it when JK Rowling said that Dumbledore was gay."
And Lewis has now issued a statement via his rep to E! News to apologise profusely for his comment.
It read: "I am hugely embarrassed that comments of mine have been linked in a negative way to Sir Ian McKellen. I have always been, and continue to be, an enormous fan and admirer of Sir Ian's.
"He's one of the greats and one of the reasons I became an actor. My comment in The Guardian was a sound bite I've been giving since 1999 - it was a generic analogy that was never intended to demean or describe anyone else's career.
"I have contacted Sir Ian McKellen and have given him my sincerest apologies."
And McKellen has brushed off the episode with a gracious tweet this morning.
He wrote: "There was no need for @Lewis_Damian to apologise to me, as I thought his comments were fair. But he's a gentleman."

There was no need for @Lewis_Damian to apologise to me, as I thought his comments were fair. But he's a gentleman.

— Ian McKellen (@IanMcKellen) December 12, 2013