The Hoops clinched their eighth successive top-flight title with a 3-0 win at Aberdeen on Saturday.
But the celebrations were marred with the sectarian slurs directed towards McInnes, who was subjected to the same abuse by Celtic fans in last month’s Scottish Cup semi-final.
The former Rangers midfielder was serving a one-game touchline ban after making gestures to Celtic supporters who branded him a ‘sad orange b*****d’.
Defending his close pal, Lennon said: “I am disappointed to say the least.
“I am disappointed for Derek, because I know what a great guy he is, he is a great football man with great integrity. I am sorry he wasn’t in the dugout today.
“I am a huge admirer of what he has done this year, and what he has done previously.”
McInnes hit out at Celtic fans’ sectarian chants and asked if the SFA were listening.
He said: “Of course I heard it because I have been hearing it for years.
“It is not if I hear it, that is not the question, the question should be are other people hearing it?
“The biggest surprise would have been if I had not heard it today, as you all know, so it is what it is.
“There has been a missed opportunity to send out the right message. I served my punishment today and I will be back in the dugout next week.”
In February, Kilmarnock boss Steve Clarke accused Rangers fans of living in the dark ages after he was called a ‘Fenian b*****d’.
“It’s lovely being back in the west of Scotland, really nice,” he said.