The Pakistan paceman, who was facing England's Nick Knight, turned to salute the cheering crowd after they saw the figures of 100.23mph flash up on the giant scoreboard.
But Rodney Hartman, World Cup communications director, said it would not be designated as official.
He told BBC Sport: "The ICC has always said there is not enough uniformity in the various speed guns around the world for any one performance to be designated official.
"What I can say is that all the speed guns in this World Cup are calibrated to measure the same rates."
It is the second time Shoaib has broken the magic mark.
"I wanted to do it and I said that before the match to the coach and the manager I wanted to do it in the second over," he said.
Shoaib explained he gains extra speed by winding his arm behind his back.
"When I get my arm back there I gain more power. It's a different action and then I just bowl quicker in the air," he added.
"When I'd done 158kph then I said, this is the time, I just cross the barrier and finish it for the rest of my life."
In April 2002, the Pakistan paceman had a delivery of 100.04mph recorded in a match against New Zealand.
But of the two guns which were installed to measure the delivery speeds, the official device broke down.
Although the Pakistan Cricket Board authenticated the achievement, many were left in doubt as to whether to trust the device which recorded the new figures.
Despite Shoaib breaking 100mph twice, the International Cricket Council refuses to acknowledge bowling speed figures.
Leading up to the tournament, many had predicted a close battle between Australia's Brett Lee and Shoaib for the title of fastest bowler.
But Lee was keen to stress it was more important to take wickets at the World Cup than to worry about bowling at more than 100mph.