Olazabal, the most recent victorious Ryder Cup skipper, finished four over and tied for 43rd place.
Irishman McGinley, who has been named captain for the next Ryder Cup, matched the Spaniard on four over.
Former Ryder Cup player Paul Casey was another casualty, failing to make it after a two-over total of 141.
Meanwhile Brooks Koepka led the way in qualifying at Sunningdale as the 23-year-old from Florida finished on five-under after the 36-hole session, one shot better than Briton Oliver Fisher.
The American turned professional after missing the cut at this year's US Open and has already won three times on the European Challenge Tour, earning his entry into the full European Tour for the rest of 2013 and the whole of next year.