Keita described his "Brother François" as the most "loyal and sincere" of French presidents in his dealings with Africa.
He thanked him for ordering the Serval military operation to fight an alliance of Islamist rebels and Tuareg separatists four years ago
"The Malian people and I, myself, will never forget what Mali owes you," he told the outgoing French president.
Hollande warned that, despite a peace deal with the Tuareg rebels, the battle against armed Islamists will be long, "because we have before us terrorist groups particularly well armed and determined to destabilise the entire region.
Inquiry into child's death to report by February
Commenting on a controversy that broke out as the summit began, Hollande promised that the results of an inquiry into the killing of a Malian boy by French troops in the north of the country will be presented "at the end of the month or at the beginning of February".
"We have nothing to hide," he said.
Earlier Defence Minister Jean-Yves Le Drian said he would "make the necessary decisions" once he had received the report.
French troops fired on a group they believed to be lookouts for an armed group, with a helicopter later returning to bury the dead boy, was "to prevent an action to strike, even kill, French soldiers in a logistics convoy", he said.
Keita warns of bloodbath in Gambia
Some 30 heads of state gathered in Bamako along with representatives of international organisations.
According to the French presidential palace, the three main topics on the agenda were the fight against terrorism, digital security and political crises in the region.
Gambia's president-elect Adama Barrow made a surprise appearance to meet west African leaders and seek their help to end the impasse in his country.
Keita called for incumbent Yahya Jammeh to step down to avoid a "bloodbath".
Barrow is due to take power on 19 January but Jammeh has refused to cede power after disputing the result of the December election.
Jammeh is seeking a court order to stop the inauguration which will be heard by the Supreme Court tomorrow.
"The Gambian voters' choice must be respected," Hollande insisted on Saturday.