The women were visibly star struck standing next to Duterte. The President hugged the first woman and gave her a kiss on the cheek before gesturing the second woman to kiss him on the lips.
After a protracted back and forth, with nervous laughter from the young woman and repeated gestures by Duterte, the President eventually leaned in to kiss the woman on the lips.
While the young woman was laughing and the crowd cheering, comments on the internet were a lot more critical.
The incident was described as "disgusting theatrics of a misogynist President" by Philippines rights group Gabriela.
The group said it was part of a bigger effort to deflect from real policy issues and Duterte's waning popularity.
"His repeated acts of machismo are meant as entertainment to hide the reality of his rapidly slipping popularity due to the issues of extrajudicial killings, the Tax Reform for Acceleration and Inclusion law and big-time corruption scandals now plaguing his rule," it said in a statement on Monday.
Duterte, who has a long-term partner with whom he has a daughter, reportedly asked the woman if she was single while onstage, CNN reported.
"Are you single? You're not separated from (your husband)? But you can tell him that this is just a joke?" he asked.
The woman, identified as Bea Kim, is married to a South Korean national and has two children. Kim said that there was "no malice" in the kiss and that it didn't "mean anything except to entertain and make other Filipinos in the gathering happy".
It is not the first time Duterte has been accused of inappropriate behaviour towards women.
In April 2016, the President spoke about the 1989 murder and rape of a female Australian missionary in Davao, where he was mayor at the time.
Earlier in 2018, Duterte told Filipino soldiers they should shoot female communist rebels in the vagina.