"We are aware that some riders were charged more than usual for rides taken from the Global Citizen concert last night, and we apologise for this," said Uber.
The company has pledged to reimburse customers.
"We understand that we went back on our promise to apply standard rates for this event, which is why we will be refunding, in full, all riders who were affected by this.
"This will not affect the drivers, who will retain their full earnings for all trips they completed.”
Witnesses described how they were left stranded outside the venue after Uber increased the prices. While waiting for alternative transport, waves of violent crime hit festival-goers.
Police have insisted that they were present, although many people have taken to social media to claim there were no police officers in sight.