The Google logo is seen at the Google headquarters in Mountain View, California. Photo: AFP/Kimihiro Hoshino
Safari - the most widely used browser on mobile devices and the default browser on iPhones and Mac laptops - is designed to block such tracking by default, the Journal said.
The Journal said Google disabled the code after the newspaper contacted it and that Google removed a message on its website saying users could rely on Safari to prevent the search giant from tracking them.
It quoted Google as saying the Journal "mischaracterizes what happened and why."
"We used known Safari functionality to provide features that signed-in Google users had enabled. It's important to stress that these advertising cookies do not collect personal information."
The Journal quoted an Apple official as saying the company was "working to put a stop" to the circumvention of the privacy settings.
The code was first spotted by Stanford researcher Jonathan Mayer and independently confirmed by Ashkan Soltani, a technical adviser to the Journal.
Google and Apple could not immediately be reached for comment.