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I had this annoying issue also.
I have managed to fix it on my system.
I looked to me as if at update was not completed.
So I looked in the Library for updates and found this update package Safari9.0.2Yosemite.pkg in /Library/Updates/031-38517
I simply ran this install package.
It took about five minutes to install on my MacBook Pro (13-inch, Early 2011), ( More than half of that time was Optimising).
After you see the message “Installation complete” Check to see if the package still exists in the /Library/Updates/031-38517 directory.
I believe this is safe to delete now.
After this I was able to run Safari from /Applications as usual.