After returning from Morocco in the early hours of the morning, Bongo presided over a ceremony at which ministers from the new government were sworn in, officials said.
The oil-rich West African state has been without an effective government for months since Bongo, 59, suffered the stroke in late October during a visit to Saudi Arabia.
After initial treatment at a hospital in Riyadh, Bongo was transferred to Morocco where he spent just over six weeks, officials said.
His return came eight days after a small group of renegade soldiers briefly tried to stage a coup before it was quashed by security forces, who arrested the leader and killed two others.
With Bongo’s prolonged absence, the country had been in limbo for months and officials at the presidential palace did not say whether he was back for good or would return to the Moroccan capital Rabat for further convalescence.
On Saturday, a new government was unveiled in a video announcement from Rabat although there were no significant changes to either the cabinet or the government.
All 38 ministers arrived at the beachside presidential palace in Libreville on Tuesday and were sworn in at a ceremony which was closed to the press, officials said.
– ‘A very difficult ordeal’ –
Bongo has not been seen in public since he was taken to hospital on October 24 in Riyadh but a video of the ceremony was released later on Tuesday.
The footage shows Bongo opening and closing the session, but there are only brief glimpses of him, shots of just a few seconds which show him seated in a wheelchair and squinting slightly.
“It was very moving to see him,” government spokesman Nanette Longa-Makinda told AFP.
“It will certainly take him several months to fully recover his physical abilities, that’s for sure,” one minister said, speaking on condition of anonymity.
“He looks like someone who has been through a very difficult ordeal,” agreed another cabinet colleague who was present at the ceremony.
So far, officials have said very little about Bongo’s health, with a presidential spokesman insisting things were back to normal.
“There can be no more talk about a power vacuum,” the spokesman said, using a phrase repeated by many ministers leaving the ceremony.
– ‘Circus goes on’ –
Before now, Bongo’s only appearance was his traditional televised New Year’s Eve address, recorded in Morocco, in which he said he had “been through a difficult period”.
Critics seized on signs of his apparent ill-health, noting the address was unusually short, his speech was slurred and his right hand seemed stiff and immobile.
His long-awaited return did little to quieten lingering suspicions among the people of Gabon.
“The circus goes on,” tweeted Marc Ona Essangui, a civil society leader.
When Bongo was first taken ill, the singular lack of official news — along with memories of the secrecy around the death of his father Omar Bongo in 2009 — had fuelled a flurry of rumours, including speculation he was incapacitated or even dead.
The Bongo family has governed Gabon for five decades, and long maintained close ties with former colonial master France.
Ali Bongo was elected head of state after his father’s death and he was narrowly re-elected in 2016 following a presidential poll marred by deadly violence and allegations of fraud.