The search engine giant launched the interactive image a day before the milestone, in celebration of the original TV show's debut on September 8, 1966.
The animation tells a short four-scene story and features some of the sci-fi series's original sound effects and iconic characters.
Google's chief doodlers Ryan Germick and Doug Simpkinson are both big Star Trek fans, and have described working on their latest project as a "labour of love", states The Hollywood Reporter.
The first Star Trek episode broadcast was titled 'Man Trap', and centred on a creature on a planet who takes control of a female archaeologist and the crew's doctor Leonard McCoy.
The official Doodle Twitter feed announced: "The 46th anniversary of Star Trek isn't until tomorrow but we wanted this one to live long(er) and prosper."
Watch a clip from the first episode of Star Trek below: