Council President Charles Tillman abstained and Ward 3 Councilman Kenneth Stokes was absent.
The amendment limits the maximum penalty for possession of 30 grams, or just over an ounce, to a $100 fine with no prison time for the first offense.
The user level amount penalty is a civil charge, similar to a traffic ticket.
Marijuana possession is still illegal in the city and state and violates federal laws.
"How we criminalize this is the issue and we must get out of the habit of turning users into criminals," said Stamps. "But giving them the appropriate treatment they need to move forward."
"It still remains illegal under Jackson city law, just a lower level of punishment, a lower fine, no jail time," explained Mississippi College School of Law professor Matt Steffey. "In a way, incidentally, it's very similar to the way state law already is for a first offense."
Jackson joins 13 other states, including Atlanta, Memphis, New Orleans, Pittsburgh and Washington D.C., which have lessen penalties for personal possession.