Go to the Apple Menu and use Software Update, enter your password and do what it says, check again to make sure it's clear.
Next look in your Applications folder for Safari and drag it's icon to the Dock, and place Safari there, it will make a new "shortcut"
If Safari is not working then
Next see if you can download the Safari from here using Firefox and install it.
If it says "can't install blah blah blah" then exit and trash the installer.
Apple issues newer Safari versions via Software update and it takes some time to get it on the web side.
But that's how you re-install Safari, however the Software update likely will fix your malware issue and provide a new Safari.
If you need Safari right away there is a way to reinstall it and all of OS X at once, quite a chore.