Mbappe was the only PSG player retained in the starting line-up after Wednesday's 2-1 win over Kawasaki Frontale in Tokyo, with manager Christophe Galtier dropping star forwards Lionel Messi and Neymar to the bench.
Mbappe alone was still too much for Urawa to handle, firing home a well-taken goal from a tight angle in the 35th minute.
Galtier brought on Messi and Neymar for the final half an hour, but neither were able to score in front of a crowd of 61,000 in Saitama.
Pablo Sarabia and Arnaud Kalimuendo got the other two goals for PSG, who play Gamba Osaka on Monday in Osaka in the final game of their tour.
Galtier handed a start to Warren Zaire-Emery -- just 16 years and four months old -- alongside Marco Verratti in midfield.
PSG made a sluggish start, and Yusuke Matsuo almost gave Urawa the lead after stealing past the defence in the third minute.
Goalkeeper Keylor Navas tipped over a shot from Atsuki Ito just minutes later but Sarabia set PSG moving in the right direction with a stylish opener in the 16th minute.
Mbappe played the ball into Mauro Icardi, who laid it off for Sarabia to lash home from just outside the box.
Mbappe then made it two in the 35th minute, receiving the ball wide on the left and cutting inside before rifling the ball past the goalkeeper.
Messi and Neymar came on in the 58th minute and the pair combined to set up Eric Junior Dina Ebimbe to put the ball in the net, only for the linesman to flag for offside.
Kalimuendo scored PSG's third in the 76th minute, moments after Nuno Mendes had hit the post.