They will be deleted unless the user returns to a Google site within the two-year period, prompting a re-setting of the file's lifespan.
The company's cookies are used to store preference data for sites, such as default language and to track searches.
All search engines and most websites store cookies on a computer.
Currently, Google's are set to delete after 2039.
Peter Fleischer, Google's global privacy counsel, said in a statement: "After listening to feedback from our users and from privacy advocates, we've concluded that it would be a good thing for privacy to significantly shorten the lifetime of our cookies."
He said the company had to "find a way to do so without artificially forcing users to re-enter their basic preferences at arbitrary points in time."
So if a user visits a Google website, a cookie will be stored on their computer and will auto-delete after two years. But if the user returns to a Google service, and each time the user returns, the cookie will re-set for a further two years.
Privacy campaigners
Privacy campaigners want to give users more control over what the search giant holds on to and for how long.
Google has pointed out that all users can delete all or some cookies from their web browser manually at any time and control which cookies from which websites are stored on a computer.
There are also tools online which can prevent the company and other firms leaving cookies on a computer.
In recent months, it has introduced several steps to reassure its users over the use of personal information.
In March the search giant said it would anonymise personal data it receives from users' web searches after 18 months.
The firm previously held information about searches for an indefinite period but will now anonymise it after 18 to 24 month
None of the other leading search engines have made any statements over anonymising IP addresses or shortening cookie lifespan.