"Service has returned to just about normal," CTA spokesman Brian Steele said.
Brown and Purple Line trains will be making all the stops in the Loop and running on the outer Loop tracks, according to Steele.
Purple Line trains are going to traveling in the opposite direction in the Loop for two days as workers finish up another portion of track repairs near the bridge.
Although the Wells Street Bridge has reopened for trains, it is still closed for pedestrians, vehicles and bikes, Steel said.
Workers were on site around the clock for over a week trying to finish the job on time. The work was nearly complete Sunday night and the track was ready to get back open for business.
Empty test trains started rolling above the Wells Street Bridge around 4:30 a.m. Soon after Purple and Brown Line trains were back on track and full of commuters who no longer had to be rerouted.
"Definitely relieved. It made late to work like six times," said Dillon Perry.
Chicago Mayor Rahm Emanuel along with CTA President Forrest Claypool and CDOT Commissioner Gabe Klein praised workers and thanked patient commuters.
The mayor who takes the Brown Line to work two days a week said he took it last week during the construction and dealt with delays in rerouting just like everyone else.
The reopening marks the end of nine days of work to replace the bridge's 500,000 pound southern half, as well as the tracks just south of the bridge.
"I'm a patient guy. I'm like, whatever needs to be done," said Jeff Brown.
Not everyone is so tolerant though. For a week and a half, CTA Brown Line users had to take shuttle buses to get in and out of the loop, as trains have only gone as far as the Merchandise Mart, Chicago Avenue on the weekends.
The Purple Line Express has not run at all during that time.
"Not too bad. I don't work in the Loop but I have appointments downtown. It was slow last week," said Robert Meyers.
The work is not done yet. The bridge will close again to Brown and Purple Line trains when the northern half of the bridge is replaced. That work will start on April 26.