The 27-year-old scored from a long kick forward in his side's 1-1 draw with Southampton last November.
His kick, after 13 seconds, caught the wind and bounced over opposite number Artur Boruc into the Saints' net.
It has now been measured at 91.9m (301ft 6in), earning it the accolade in the record book's latest edition.
"I feel amazing to be honoured in this way and as a goalkeeper I didn't expect this to happen, not for this type of record anyway," the Bosnia and Hercegovina international told Stoke's official website.
He added: "I will take it though and enjoy it."
Begovic joined an exclusive club of goalkeepers to have scored in the Premier League when finding the net against Southampton.
Peter Schmeichel, Brad Friedel, Paul Robinson and Tim Howard are the others with goals to their name.
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Stoke City goalkeeper Asmir Begovic has earned a place in the Guinness World Records book for the longest goal scored in football.