It was the first gold medal of the World Athletics Championships as Kibet, 24, crossed the line in 2:15.59 sec.
Kenyan-born Shami, now running for Qatar, clocked 2:17.18 with Switzerland's Viktor Rothlin kicking hard to take third in 2:17.25.
The last Kenyan to win the title was Douglas Wakiihuri in Rome in 1987.
It was a slow time as the mercury soared to 30 C by 8:00 am, and coupled with 60 percent humidity the conditions were gruelling. They took their toll with Ugandan Amos Masai stretchered away near the finish after collapsing.
With Morocco's Jaouad Gharib, the double defending champion, out injured, the door was open for any number of athletes to make a name for themselves and Kibet grabbed the opportunity.
It was his second career marathon victory, after winning in Vienna earlier this year.
A pack broke away in the first 10 kilometres, led by Kenyan William Kiplagat and Ethiopians Gudisa Shentema and Ambesse Tolosa, with Spain's Jose Rios and Eritrean Yared Asmerom close behind.
By half-way the cream was rising to the top with nine runners all clocking 1:08.29, led by Uganda's Alex Malinga who had Kiplagat, Rios and Tolosa hard on his heels as they pounded the streets of Osaka.
Kibet was in 28th, but in touch. And Japanese runners were keeping pace with the consistent Tsuyoshi Ogata, a former world championships bronze medallist, boosting local hopes of a medal on the first day of competition.
But by 30 kilometres, Kibet had made the break, putting 10 metres between himself and the chasing Kiplagat and Shami.
Kibet had a steely look in his eyes and the gap between him and the rest of the field continued to open with the race on for silver. Shami, the Asian Games champion, showed his mettle to come second.
An exhausted Kiplagat faded badly to finish eighth and had to be helped from the stadium.
Asmeron came fourth with Ogata fifth.
Last Mod: 25 Ağustos 2007, 15:55