Metra said the real test on the app's ability to handle operations will be during the Monday commute.
Problems with the app came as a number of system and fare changes went into effect on Feb. 1.
There was also an increase in purchase volume from the app users, Metra spokesperson Meg Reile said. The real test, she said, will come during the Monday commute.
Metra said the app currently has no known issues.
"Metra's mobile app vendor has worked diligently through the weekend to correct the issues from last week," a Metra alert to customers read. "At this point, the vendor is confident the app will perform as intended, in advance of tomorrow's morning rush-hour."
The outage had expanded on Friday as it impacted Chicago Transit Authority, Metra and Pace passes and tickets, Ventra said.
The outage came one day after Metra rolled out a new fare structure.
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Friday morning train commuters had trouble purchasing new Metra, CTA and Pace mobile tickets. Some also were having problems launching already purchased tickets, according to Metra.
"Riders unable to make purchases will be accommodated by transit personnel on buses, at rail stations and on the trains. We apologize for the ongoing inconvenience," Ventra said.
"Any pending charges should be dismissed by your bank before posting to your account," Metra stated. "If a charge is posted but no ticket is populated, then contact Passenger Services at 312-MY-METRA (696-3872)."
Metra conductors were instructed to accommodate riders onboard. The rail agency took away any remaining ticket windows Thursday in an effort to push riders to use the Ventra app.
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"When I came down here to come to work, it wasn't working," commuter Brannen Nelson said. "I have the app on my phone but I have (a card) too because I know sometimes (the app) doesn't work."
CTA issued a statement apologizing and saying in part, "Transit personnel will be prepared to accommodate any riders unable to purchase fares through the Ventra app."
Metra issued an apology to customers saying the vendor behind the app, Cubic Transportation, is working to solve the problem that started as many passengers tried to purchase their monthly tickets Thursday amid a new fare structure. That outage intermittently affected CTA and Pace riders as they tried to load more funds to the app Friday.
"It is frustrating. We've done a lot of work to be ready for today, and it's frustrating that this technological problem comes up," Metra spokesperson Michael Gillis said.
Plus, the 10-ride ticket has been replaced with a five-day pass. There is also a new program for low-income riders on all lines.
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All SNAP recipient household members living in Cook, DuPage, Kane, Lake and McHenry counties are eligible. For more information, visit fares.rtachicago.org.
Metra said with the loss of first of the month fares and those this morning, Cubic Transportation could be on the hook for as much as a $1 million in lost fares.
Visit metra.com to see the full list of changes.