The American singer distributed crayons and colouring books to children at the Villamor Air Base grandstand, where evacuees from eastern Leyte and Samar provinces arrive via C-130 planes.
Social Welfare Department officer Jane Abello says Keys stayed for about half an hour to chat with evacuees.
The R&B star was in Manila for a concert on Monday at the seaside MOA Arena.
The Philippine Star earlier quoted her as saying that "music has a way of lifting your spirit and that's what I hope to do for the Filipino people."
Keys tweeted three days after the 8 November typhoon: "To the people of the Philippines my heart is with you."
She also encouraged fans around the world to donate to the typhoon victims.
I'm so grateful I was able to come to the Philippines and spend some time with some of the most resilient, beautiful spirits I've ever met.
— Alicia Keys (@aliciakeys) November 25, 2013
Today was next level. Thank you for your inspiration!
— Alicia Keys (@aliciakeys) November 25, 2013