Bidding Eubanks farewell on Friday's show, Leno said, "I don't think we've ever had an argument."
The other five members of the Tonight Show Band will also be leaving with Eubanks.
Eubanks performed as Leno's comic sidekick and guitarist. The 52-year-old had been aboard since Leno took over NBC's "Tonight" in 1992. Eubanks became musical director when Branford Marsalis left in 1995.
In April, Eubanks announced his plans to depart, explaining he wanted a career change of pace.
He will be replaced by former "American Idol" music director Rickey Minor, who arrives with his own troupe June 7.
"The Tonight Show" will air reruns next week.
