Bekele, just turned 22, had been hoping to complete an historic double of his own.
Silver went to Ethiopia's Bekele, a meter back, with 19-year-old world champion Eliud Kipchoge of Kenya taking bronze.
Kenenisa Bekele's brother Tariku took a deserved win in 7:38.98 ahead of Kenyans Edwin Soi and Isaac Songok.
And Kenenisa Bekele was still struggling to find his form after the death of his fiancee this year.
Gebre Gebremariam and Dejene Berhanu have been recruited to strengthen the meeting, following the withdrawal of countryman Kenenisa Bekele.
ATHENS, Greece -- Hicham El Guerrouj completed an historic Olympic 1, 500-5, 000 meters double after a battle royal with Kenenisa Bekele.
"The court of appeals missed a chance to right a terrible wrong, " Africa director Daniel Bekele said in a statement.
Bekele burst past with 200 to go, Kipchoge flailing desperately on his inside and Guerrouj smoothly making ground on the outside.
Bekele was beaten only once in 2004, when he finished runner-up to Moroccan Hicham El Guerrouj in the Olympic 5, 000m final.
Also confirmed for Birmingham are former Olympic triple jump champion Christian Olsson and current 1500m and 10, 000m Olympic champion Kenenisa Bekele.
Olympic 10, 000m champion Bekele pulled out following the death of his fiancee.
Ethiopia's world and Olympic 10, 000m champion Kenenisa Bekele put in a fierce final sprint to see off Kenyan Isaac Songok in 12 minutes 48.25 seconds.
For most, Bekele, a man of huge ambition and pride and already being touted as one of the greatest of all time, had started as favorite.
But fellow Ethiopian Markos Geneti appeared ominously on Bekele's shoulder with two laps to go before surging past him at the bell to win in 8:14.28.
Alem Tachale, who was due to marry Bekele in May, collapsed while on a training run with him on the outskirts of the Ethiopian capital Addis Ababa.
Ethiopia's Bekele, who claimed an unprecedented long-distance double with golds in the 5, 000 and 10, 000m in Berlin, rounded off a spectacular season with victory in the 5, 000m.
The race was a re-run of the world championships 5, 000 last year when Bekele and El Guerrouj had approached the starting line having both won their earlier events.
Before Dibaba, the great Kenenisa Bekele -- a three-time Olympic champion and double world record-holder in the 5, 000 and 10, 000m -- was the most famous product of the area.
Gebremariam was second in the 2004 World Cross Country Championships behind Bekele, while Berhanu ran the fastest half marathon ever on British soil to win last September's BUPA Great North Run.
Meanwhile, Kenenisa Bekele - Olympic champion in the 5, 000m and 10, 000m - won the 5, 000m event in a time of 12 minutes 50.18 seconds ahead of Moses Kipsiro of Uganda and Kenyan Moses Masai.
Among the international stars on show on Sunday are Ethiopian Kenenisa Bekele, who goes in the 3, 000m and 5, 000m, and Russia's dethroned world champion Yelena Isinbayeva, who goes head-to-head with her Polish successor Anna Rogowska in the women's pole vault.
Bekele, a two-time winner when the event was staged in Newcastle, is scheduled to run in the Boston Indoor Games on 29 January, the Norwich Union Grand Prix in Birmingham in February and the World Cross Country Championships at the end of March.
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