Alex Iovine, 26, and Emma Pichl, 24, have been dating for nearly two years and were heading back to Manhattan last week after celebrating a friend's birthday at a bar.
Iovine told CNN she and her girlfriend were sitting on opposite sides of the back seat when they kissed.
"The middle seat was open. We were just having a conversation throughout the ride and, at one point, we leaned over into the middle and peck-kissed," Iovine said. "That's genuinely all it was."Read | A platform that redefines portrayal of lesbian relationships
Uber has listed community guidelines on its website, which specify that "you shouldn't touch or flirt with other people in the car" and that there's "no sexual conduct with drivers or fellow riders, no matter what".
But both Iovine and Pichl said they kissed once and were not touching inappropriately.
"We understand that someone would feel uncomfortable if people were making out in the car," Iovine said. "But that's not what was going on here."
The two women said several minutes after their peck, the driver pulled over onto the side of a Manhattan road, away from their destination, walked over to the rear passenger side door and opened it, telling them to get out.
He told the women that such kissing was "illegal" and "disrespectful". El Boutari told the New York Daily News that he was uncomfortable with the couple's behaviour in his car on the whole, not just with the kiss.
He said they played loud videos on their phones and that one of the women put her feet up on the seats.
However, Iovine told the Daily News they didn't behave inappropriately. Both the driver and the riders reported the incident to Uber.
The women told CNN Uber refunded their $15 fare. Uber spokeswoman Susan Hendrick said that the company removed the driver's access to the app and that it was investigating the incident.Read | Ariana Grande thanks LGBTQ fans in open letter
"Uber does not tolerate any form of discrimination and we have been in touch with the rider regarding her experience," Hendrick said.
Iovine and Pichl said the incident changed their perspective on being in a same-sex couple in New York City. They now plan to attend the city's June 24 Pride parade, which celebrates the LGBTQ community.