The pyre that was kindled in the capital Libreville represented the west African nation's entire government stockpile and would have required the killing of some 850 elephants.
"Gabon has a policy of zero tolerance for wildlife crime and we are putting in place the institutions and laws to ensure this policy is enforced," Bongo said.
"We don't want our children to inherit an empty forest. For that reason, we cannot allow this trafficking to continue," he said.
The spectacular burning of ivory tusks and carvings at Cite de la Democratie, a vast complex for hosting state functions, was welcomed by conservationists at a time when elephant poaching in central Africa is reaching record levels.
The stock destroyed Wednesday amounted to 4,825 kilograms, including 1,293 pieces of rough ivory mainly composed of tusks and 17,730 pieces of worked ivory, according to the WWF nature protection organisation.
"We believe this is a strong signal of intent by Gabon against poaching and illegal wildlife trade -- at a time of intense poaching pressure in central Africa, where the illegal killing of elephants for ivory is at record levels," the WWF said.
Some of the ivory burnt on Wednesday was up to a decade-old but most of it was seized from poachers over the past five years, said Lee White, who heads the National Parks Agency (ANPN).
"If we're not careful, one day we'll end up having to go to zoos abroad to see animals that are originally from here," he said.
There are an estimated 30,000 elephants in Gabon.
"This is an international problem and Gabon is coming under siege by criminal gangs of hunters and crime syndicates that smuggle ivory to Asia," White said.
"Unless there is a strong international reaction to stop wildlife crime, and ivory smuggling in particular, the forests of Gabon will no longer vibrate with the rumble of the forest elephant."
WWF's Carlos Drews told AFP that one of the reasons for burning the stockpile was to prevent any of the confiscated ivory from leaking onto the illegal market.
"So we destroy it the same as we destroy cocaine in Latin America," he said.
According to the ANPN, the total value of the ivory that went up in flames Wednesday is Libreville is around 7.5 million euros, or close to $10 million.
Ali Bongo called for tougher action to put the squeeze on the Asian market, where elephant tusks are carved into ornaments and fetch around $2,000 a kilo.
"The moment demand disappears, so will the offer. It is vital we all apply pressure on these countries so that they understand how dangerous what is happening now is for our countries," he said.
Rhinoceros horns are even more sought after in Asia, where they are believed to hold medicinal properties that can cure ailments, including cancer, despite ample scientific evidence to the contrary.
A report issued last week by the UN body that regulates the international wildlife trade -- the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) -- said 2011 was the worst year on record for elephant poaching in Africa.
It is estimated that tens of thousands of elephants are being killed across Africa each year.
In southern Africa, ivory trafficking is run by crime syndicates that are armed and well-equipped. Some poachers use helicopters to hunt their prey.
The World Wildlife Fund's Carlos Drews stressed that poaching and ivory trafficking should be understood as a serious crime with consequences reaching far beyond the fate of wildlife.
"This illegal ivory when it is sold is fueling rebel groups, civil wars in central Africa. It destabilises society. There are human lives involved, rangers are being killed," he said.