Two members of council, Mayor Naheed Nenshi and Ald. Brian Pincott, were out of town during Tuesday's vote.
Earlier in the day, city council considered and rejected by a vote of 8-5 putting the fluoride issue to a plebiscite during the 2013 municipal election.
Council also rejected the idea of referring the matter to an expert panel.
The issue has proved a lightning rod for Calgarians, and past plebiscites have revealed public opinion is nearly even split on the matter.
In 1989, 53 per cent of Calgarians voted in favour of adding fluoride. Two years later, it was added.
After a well-attended, all-day public meeting late last month, the removal of the chemical was recommended to council by a city committee.
On Tuesday, council also supported using some of the savings of removing fluoride to examine ways of improving dental health for children living in poverty.
Proponents of fluoride say it prevents tooth decay, especially in vulnerable groups such as the poor, children and the elderly. Opponents question the safety of fluoride in drinking water and suggest it should be up to individuals to decide whether to expose themselves to the additive.
Ald. Druh Farrell, who led the anti-fluoride charge, said helping families who can't afford fluoridated toothpaste is a better idea than medicating the entire population.
"It's not our responsibility, but what we've said is because we had this responsibility and because children in poverty are used as a reason to support fluoride, then let's really help those children," she said.
Ald. Jim Stevenson said there's insufficient medical proof that keeping it in the water has any benefit.
"We as a council have to show some leadership here. We have no right to force this right on all Calgarians. I would really question our right to put it in, but … I don't question at all our right to remove it," he said.
The timeline for the removal of fluoride remains unclear, as the city must apply to Alberta Environment to amend its water licence.
The city should also see cost savings in the move — the cost of adding fluoride to Calgary's water is about $750,000 per year.
The city was also facing $6-million upgrades to the Bearspaw and Glenmore water-treatment plants needed for the fluoridation process in the near future.