Comolli officially left Anfield by mutual consent in 2012 citing family reasons, although rumours suggested he was shown the door over failings in the transfer market.
The Frenchman now claims he was sacked and feels the initial negative reaction to the signing of Henderson - now Liverpool vice-captain - was behind his dismissal.
"When we signed Jordan Henderson, he got so much criticism, I got so much criticism," he said at the Web Summit in Dublin.
"I was never told why I was sacked but I was led to believe it was because we signed Jordan Henderson, and the owners were convinced he was not good enough."
Henderson reportedly cost up to £20 million when he arrived from Sunderland in 2011, but failed to capture the imagination during his early days on Merseyside.
However, the 24-year-old has become a key figure under manager Brendan Rodgers and Comolli insists he always saw the potential.
"Looking at Jordan Henderson, we wanted legs, we wanted physicality, we wanted pace and creativity in the final third," he added. "I was able to benchmark Jordan against the top midfield players in the Premier League, taking his age into consideration, taking the transfer fee into consideration, and in my position, you need to look at age, money and the player’s ability.
"Looking at all this, what he was doing for his age, and all due respect to Sunderland, he was definitely undervalued by the market. And I've been told we overvalued him. Even directors at Sunderland later said 'You didn't know what you were doing'.
"Jordan stood out at the time, when he was 20, because of the number of chances he created in the final third. He was very good at it. When you look at chances created in the final third in open play, you are the best player finishing in the top 5-10 [in the Premier League] every year.
"So when I saw Jordan in that area, I thought he's definitely got something. Because when I was looking at it five years back, [Thierry] Henry, [Frank] Lampard and [Cesc] Fabregas were there, so when he was there, I thought definitely he's got something. It can't be a coincidence, and now look at him."
