Kipchoge ran down the race favourites to steal the gold medal in a championship record 12:52.79 with a desperate dip for the line.
El Guerrouj and Bekele, both looking to be crowned dual gold medallists having won the 1500m and 10000m respectively, had to settle for silver and bronze.
Bekele set the early pace, going through the first kilometre in a fast 2:31.94, world record pace. Following his every move was El Guerrouj, running in his first championship 5000m.
The four Kenyans - Richard LIMO, Abraham CHEBII, John KIBOWEN and Kipchoge - were also in the mix as the field began to string out.
At 2000m (crossed in a slower 5:07.27) Bekele still led but was watching the action behind him on the big screen.
The placings remained much the same until the third kilometre when Kipchoge moved to the front. Bekele jumped back in front after nine laps with El Guerrouj once again following.
The Ethiopian tried to get another runner to take the lead but no-one seemed interested until finally, with the pace slowing, Kipchoge took charge going through 4000m in 10:28.46.
Here El Guerrouj made his move and now it was Bekele who was the shadow with Kipchoge, Limo and Chebii not far behind.
On the bell lap El Guerrouj and Kipchoge forged ahead while Bekele and Chebii followed. It was now a race in four as they went down the back straight.
It was Chebii, known for his fast finish, was the first to wilt, as he didn't quite have the pace to challenge.
El Guerrouj led into the home straight but Kipchoge and Bekele were staying with him. Bekele out in lane three couldn't match the speed of the 1500m world champion but Kichoge was able to reach El Guerrouj's shoulder. Pressured to hang onto his lead, El Guerrouj began to falter and Kipchoge out-dipped him for the world title, giving Kenya just it's second gold medal of these championships.
El Guerrouj's time of 12:52.83 would have won him gold at any other World Championship. Bekele, considered to be the heir to world record-holder Haile GEBRSELASSIE's (ETH) throne, clocked 12:53.12 for the bronze medal.
Back in fourth place was John KIBOWEN, bronze medallist in 2001, who ran a personal best 12:54.07.