Both sites attracted 18 percent more European surfers compared with the figures for August.
Wikipedia attracted 59.9 million European visitors in September, while YouTube recorded 27.4 million.
The other big winner was the education sector, as millions of children returned to school across Europe.
Traffic to education sites gained 11 percent overall. The BBC Learning site jumped 97 percent with 2.2 million visitors, and MSN Encarta soared 33 percent with 2.1 million visitors.
Google, Microsoft and Yahoo retained their rankings as the top three sites for European Internet users.
However, the sites all showed a flat performance with just a one percent rise in traffic.
Google pulled in an audience of 160.8 billion, Microsoft 146.1 billion and Yahoo 100 billion, out of a possible 216.2 billion European surfers aged 15 and above.
The figures in the study exclude traffic from public computers such as internet cafés or access from mobile phones and PDAs.
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