Cal was fourth last year, behind MIT, but the two schools swapped places in this year's list, which is compiled by Shanghai Jiao Tong University.
"Berkeley is again the top-ranked public university, followed by UCLA (12th), UCSD (14th) and UCSF (18th)," the campus announcement said.
Eight of the top 10 were U.S. institutions, joined by Cambridge and Oxford in the UK. This list shows the top group and their scores:
2. Stanford, 72.6
3. Berkeley, 71.3
4. MIT, 71.1
5. Cambridge, 69.6
6. Cal Tech, 62.9
7. Princeton, 61.9
8. Columbia, 59.8
9. Chicago, 57.1
10. Oxford, 55.9
The methodology used to compile the ranking weighs "quality of education (worth 10% of the total), quality of faculty (40%), research output (40%), and per capita academic performance (10%)," the UC Berkeley announcement said.
The only Asian schools in the top 100 were three from Japan: University of Tokyo (21st), Kyoto University (26th) and Osaka University (85th).
Canada had four universities in the top 100: University of Toronto (28th), University of British Columbia (40th), McGill University (58th) and McMaster University (92nd).
More information about the criteria used in the rankings can be found on the Shanghai Jiao Tong University website.