Connolly, once a regular at the pub, said the Clutha would always have a special place in his heart as he recalled the fond times he had there.
The actor and comedian said he had never before been moved to pay tribute at the scene of a tragedy, but felt he should mark the occasion.
He laid a bouquet of white lillies, white roses and green ferns at the crash site. A card attached read "Rest in Peace friends, Billy Connolly".
Connolly, recently given the all-clear from prostate cancer, said: "It's very sad but it means quite a lot to me. I have played in all of these pubs. The Clutha was a good music pub. They didn't mind banjo players, which makes a change. I had many happy times in there."
The comedian, affectionately known as the Big Yin, regularly played at the venue in the early 1970s, when it was known as The Wee Man, with the late Gerry Rafferty and their band The Humblebums.
It was also a favourite venue for him when he was starting out as a comedian.
Connolly said he had watched the event unfold on television in New York.
He added: "Glasgow has really risen to the occasion. I have never heard so many nice things about Glasgow.
"I had to do something; I couldn't just let it pass, though I have never done anything like this before.
"I was devastated to hear of what happened, like anyone else. It was weird seeing it happening on TV while I was in New York."
"Everybody's talking about how well Glasgow coped. I was very, very proud to be a Glaswegian.
"The Clutha's got a very special place in my heart."