The world champion, 28, who has not lost an international match since August last year, defeated the champion of four years ago, Mongolia's Tuvshinbayar Naidan, who left the arena at London's ExCel Centre on a stretcher, with an automatic winning ippon throw.
Khaibulaev , a native of the mainly Muslim southern Russian region of Dagestan, praised Russia's most powerful man for his support.
"He (Putin) said to me thank you for the victory," Khaibulaev told reporters as he walked out, still gleaming after his encounter with Putin.
"He has been cheering for us for four years now and he really cares for the sport. I am so happy I managed to make him happy," he said.
Khaibulaev only reached the final after a tight contest with Germany's Dimitri Peters was decided by judges after it finished scoreless.
"The German was very tough," he said.
Earlier on the other top seeds fell early with world number one Kazakh Maxim Rakov losing in the first round to outsider Elmar Gasimov of Azerbaijan, Japan's Takamasa Anai, the 2010 world champion, ousted in the last 16 and Henk Grol of Netherlands vanquished in the quarter-finals.
Grol came back to beat 34-year-old South Korean Hwang Hee-Tae to win a bronze to add to the one he got in Beijing in 2008, delighting a huge Dutch contingent in the crowd.
Germany's Peters, 28, took the other bronze beating Uzbek Ramziddin Sayidov, the reigning Asian champion.