"The Electric Zoo organizers have worked with city officials to reduce health risks at this event, but in view of these occurrences, the safest course is to cancel the remaining day of the event," the city said.
Police identified those who died as Jeffrey Russ, 23, of Rochester, N.Y., and Olivia Rotondo, 20, of Providence, R.I. Rotondo was attending the University of New Hampshire and was not known to do drugs.
In addition to the two deaths, at least four other concertgoers remain in the hospital in critical condition.
The cause of death for the two "Electric Zoo" attendees is believed to be connected to the drug MDMA which can be consumed in ecstasy pills or in its pure crystal form, known as Molly.
The last day of the festival featured high-profile acts including Avicii, David Guetta and Diplo.
The Electric Daisy Carnival moved out of Los Angeles to Las Vegas in 2010 after a 15-year-old girl died of an apparent drug overdose.
The Associated Press contributed to this report.