The resignation came hours after the African Union had suspended Togo on Friday in the latest blow to Gnassingbe.
Shortly after Gnassingbe's announcement, Abass Bonfoh was elected chairman of Togo's national assembly and took over as the country's interim president.
A special session of the national assembly elected Bonfoh, the sole candidate, by 57 votes to four with one abstention to replace Gnassingbe.
African leaders, European officials and the United States had all urged Gnassingbe to quit since he was appointed president by Togo's powerful army soon after his father, Gnassingbe Eyadema died on 5 February, ending his 38-year rule.
Under Togo's constitution, the head of the national assembly should have become the acting president on the death of Eyadema.
But the army named Gnassingbe president and Togo's national assembly elected Gnassingbe as its head making him the legal interim president.
Gnassingbe said he was quitting to ensure transparency in forthcoming elections.
"In order to guarantee the transparency of this election ... and to give the same chance to all the candidates, I have decided to renounce the post of president of the national assembly, who is acting president of the republic," Gnassingbe said in a speech on state media.
"It's now up to the national assembly to elect a new head who will be interim president of the republic," he said.
In a bid to stem international fury, Gnassingbe had pledged to hold presidential elections in 60 days but he indicated he would stay on until then, drawing international anger.
"I sincerely hope that the West African community and the international community remains at our side to guarantee the organisation of free, transparent and honest elections," he said in the speech.
Earlier on Friday, Gnassingbe was named the ruling party's candidate in forthcoming presidential elections.
Togo's main opposition parties have demanded the reinstatement of the head of the national assembly, Fambare Ouattara Natchaba, who should have taken over on Eyadema's death.