Jones, 27, was stripped of the UFC title on Tuesday after appearing in court on a felony first appearance related to a hit-and-run incident he was allegedly involved in over the weekend in Albuquerque.
Johnson (19-4) was supposed to challenge Jones (21-1) for the title at UFC 187 on May 23 in Las Vegas. The UFC removed Jones from the card on Tuesday. Johnson will now fight Daniel Cormier (15-1) for the vacant light heavyweight championship.
"I can say that I'm kind of disappointed with the mistake Jon made, but he is human," Johnson told ESPN.com. "I definitely wanted to fight him for the title. He's the best. Everybody wants to fight the best if you're in this sport for the right reasons.
"But I can't be too disappointed. I have a title fight and a worthy opponent in Daniel Cormier. I'm happy I get to fight someone like him."
In addition to being stripped of the title, Jones has been indefinitely suspended by the UFC.
Jones did not enter a plea during his court appearance on Tuesday. He is charged with leaving the scene of an accident involving death or personal injury. The felony charge carries potential jail time.
According to Bernalillo County Metropolitan Court spokesperson Camille Cordova, the District Attorney has 60 days to move the case forward.
Johnson said he expects Jones, who owns the record for consecutive 205-pound title defenses with eight, to eventually bounce back from the incident.
"I think he'll come back and I think he'll be twice as dangerous," Johnson said. "You know how he is. When you think he can't do something, he shows you what he can do. I know he'll be back and he'll be ready. And so will I.
"He's still the same guy. I wrote on Twitter last night that regardless of everything, he's still the greatest light heavyweight champion of all time. I have nothing against him. What he did was not the brightest thing, but he is human and young."
Turning his focus to Cormier, a former U.S. Olympic wrestler, Johnson said nothing significantly changes in his preparations.
Fighting out of the Blackzilians camp in Boca Raton, Florida, Johnson had flown in several international kickboxers to emulate Jones' striking. He said he would continue working with those sparring partners, though he might add other wrestlers.
"Mentally and physically, I'm here," Johnson said. "As far as training partners and stuff, I'm going to keep working with those guys. But I'll need some short, scrappy wrestlers. I'm not worried about anything.
"I'm excited. Fans should be excited. It's still a great matchup. Everybody was looking forward to Jon Jones. So was I. But trust me, this fight (with Cormier) will be amazing."