The Mission: Impossible star picked up the six-year-old in New York after flying in from California where he has been filming new movie Oblivion.
The two were last seen together a month ago in Iceland.
The reunion came hours after Katie and Suri were involved in a car accident when a rubbish truck reversed into their chauffeur-driven Mercedes after Katie had just collected her daughter from a gymnastics class in Manhattan. Both mum and daughter were unhurt.
"It was nothing major other than the fact that it was Katie Holmes," said a witness at the scene.
Tom and Katie agreed the terms of their divorce, including the custody arrangements for Suri, in just two weeks after five years of marriage.