The ban passed by a vote of 6-0, with Mayor Glen Robertson leaving the meeting early.
Thursday's vote caps a months-long debate over the issue, brought on in large part by Gina Johnson.
Johnson is a concerned mother who has spoke against the substance at multiple city council meetings.
After Thursday's vote, Johnson said she was happy with the council's first step but she said more must still be done to education local youth about the dangers of synthetic marijuana.
Council members did amend the ordinance to take out a provision that would have banned substances with a chemical similar to marijuana, which means substances with a chemical makeup similar to synthetic marijuana will still be allowed.
Local head shops and other stores that sell the substance have thirty days to get rid of their inventory.