The water to be disinfected is from the district's North Side and Calumet plants.
In addition to the Chicago River, the Cal-Sag Channel and the Little Calumet River will become cleaner.
Environmental groups are hailing the decision as a new chapter for the waterways.
"We are thrilled. This a wonderful day, a wonderful opportunity. And I look forward to sharing the river with all of you," said Margaret Frisbie of the Friends of the Chicago River.
"Today is not just a huge day for us in the city but for future generations. I look forward to my kids, who are 2 and 7 months old, now are able to recreate without any concern about our waterways," said Michael Alvarez, Water Reclamation District commissioner.
"We are going to be improving water quality for pennies per household. It's really an insignificant amount when you think of the huge investment to improve our environment," said Cynthia Santos, Water Reclamation District commissioner.
The action comes after Senators Durbin and Kirk toured the river last month asking for a cleaner waterway. Also, a letter from the EPA directed local officials to disinfect the sewage.
"I'm so pleased we are moving in this direction. Our talented, smart, capable staff will be investigating technologies to do this," said Debra Shore, Water Reclamation District commissioner.
"I think today is a first day of a new era when we view the Chicago River not as a conduit to get sewage out of Chicago as fast as we can, but as a green, cool, clean urban waterway that we can all celebrate and enjoy in total confidence," said Jack Darin, Sierra Club.
The vote is just the first step in cleaning up the river. A plan and funding are still needed. The system is expected to cost $240 million to build and $26 million a year to maintain. It's not clear where the money will come to pay for the cleaning process.
Hearings will give the public a chance to be heard before the plan takes effect.