A Los Angeles judge ordered Lee to stay at least 100 yards away from Chappelle and the venue where the attack occurred.
His bail was set at $30,000 for the multiple misdemeanor charges, with a bail review hearing set for early next week.
Lee has been identified as the man seen on video rushing the stage as Chappelle performed Tuesday night as part of the "Netflix Is a Joke" comedy festival. He tackled the comedian before security swooped in, rushed him to the side of the stage and subdued him.
Police say Lee was carrying a replica handgun with a large blade that folded out like a pocket knife. It did not appear he used the knife in the attack.
The office of Los Angeles County District Attorney George Gascon reviewed the case and determined it did not meet the standards for a felony prosecution, referring it as a misdemeanor case to the Los Angeles City Attorney's Office.
Chappelle's lawyer Gabriel Colwell told Rolling Stone: "We request that DA Gascón reconsider, correct this mistake and charge this as a felony. This is what Mr. Chappelle wants. Mr. Chappelle wants this case charged as a felony.
"Entertainers in Los Angeles need to know that the justice system will protect them on stage," he said.
City Attorney Mike Feuer's office filed four misdemeanor charges: battery, possession of a weapon with intent to assault, unauthorized access to the stage area during a performance and commission of an act that delays an event or interferes with a performer.
If convicted on all counts, he could face up to 18 months in county jail and/or up to $4,000 in fines, according to the city attorney's office.
It was not immediately known if Lee has had retained a lawyer, and the motive for the attack was unclear.
In the meantime, Kevin Hart is joining other comedians in condemning the attack.
Appearing on "Jimmy Kimmel Live" on Thursday night, Hart said: "We've now lost sight of the relationship of audience to comedian, and that line has gotten blurred to where it's like, 'Well, I don't need to do this and like this, and I can stand up and make a point.'
"It becomes a hard case of, why did you come? Why did you buy a ticket if that was your want or need? When I say we need to get back to the place of respecting the entertainer, respect the craft," Hart said. "If you're coming, come to have a good time and enjoy the person that you saw. If you have no interest in that, you don't have to buy a ticket. You don't have to go."
LA comedy clubs beef up security after man tackles Dave Chappelle on stage at Hollywood Bowl
People standing in the wings of the stage, including actor Jamie Foxx and rapper Busta Rhymes, rushed on to the stage to try to help Chappelle.
Security guards chased and overpowered Lee, who was taken away in an ambulance for treatment of an unspecified injury.
"The performances by Chappelle at the Hollywood Bowl were epic and record-breaking and he refuses to allow last night's incident to overshadow the magic of this historic moment," Chapelle's publicist Carla Sims said in a statement.
Chappelle was attacked as he was wrapping up a routine in which he talked about how comedians have to worry more about their personal security in the wake of this year's Academy Awards ceremony where the Oscar-winning actor slapped Chris Rock on live television in reaction to a joke about his wife.
Rock was also in the wings of Chappelle's show, He grabbed the mic and jokingly asked, "Was that Will Smith?"
The Associated Press contributed to this report.