But the continental body face new challenges added to existing ones Faki was confronted with when he was elected to the post four years ago.
The former Chadian diplomat secured 51 votes out of 54 during a closed-door meeting of heads of state and government whose preoccupation has been how to tackle the coronavirus and deal with its deleterious aftermath to national economies.
There were 3 abstentions during the vote to retain Mr. Mahamat.
His reelection comes against the backdrop of the protracted fight against the ongoing second wave of the rampaging coronavirus pandemic.
While on the cusp on reelection, the continental death toll had jumped in recent weeks, more than at any one time since the pandemic hit AU countries in the early months of 2020.
The continent has recorded well over 2 million Covid-19 cases with some 71, 000 deaths and just over 1,900, 000 recoveries since the disease was first reported in Egypt in February 2020.
Naturally Faki's bid for reelection, had emphasized the need for Africa not to be left behind in the race to secure enough vaccines to treat its rising cases.
Now it is up to him to make good on this promise but the signs have been encouraging to the dispassionate observer.
Last month it was reported that the African Union secured one billion COVID-19 vaccine doses for its member countries.
According to South African president Cyril Ramaphosa who chaired the AU throughout last year, the doses are from Pfizer, AstraZeneca, through the Serum Institute of India, and Johnson & Johnson.
By his projection, the 270 million doses are being rolled out across Africa this year with at least 50 million being availed the continent between April and June.
But many say with the growing number of cases everyday, Africa as a single bloc would need more doses.
Ramaphosa's South Africa has the greatest number of Covid infections, hence the high stakes being placed on efforts to secure the jabs which could not only save millions of lives but stave off further infections.
But the vaccines has hit some snags in South Africa where their use are being put on hold due to their effectiveness in face of a new variant of the coronavirus which have been detected in a number of other African countries including Malawi.
The vaccination exercise was due to begin in South Africa next week but this has been thrown into doubt.
In view of growing concerns over vaccine nationalism which threatened the equal distribution worldwide, Ramaphosa with help from Faki's AU set up the Africa Vaccine Acquisition Task Team (AVATT), which had been instrumental in securing the doses.
While the world's prosperous nations have been n front of the queue to secure billions of doses of anti-Covid vaccines for their citizens, those in Africa had watched from the sidelines apparently powerless to join in the scramble.
But rolling out the AstraZeneca/Oxford or AZD1222 vaccine will have to depend on WHO medical clearance for emergency use.
The WHO have put the vaccine under review and will communicate the outcome in the next few weeks if not days.
What his words had implied was that so far the continent has been left behind in this global race which many say is heavily skewered in favour of rich nations, Faki has another four years to help plot the continental medical response to the pandemic.
Meanwhile Faki also faces the challenge of finally setting in motion the Africa Continental Free Trade Area which is scheduled to begin this year.
Trade barriers still very much in evidence across Africa, a year after over 20 countries on the continent ratified the agreement that would open up impediments to the free movements of peoples and goods.
The AfCFTA is about reducing tariffs and non-tariff barriers, facilitating free movement of people, goods and services, right of residence and investment.
The African Union under Faki faces several challenges including protracted negotiations on its protocols, the annual infrastructure deﬁcit running into $108 billion according to a 2018 African Development Bank review and the reluctance of countries to close their borders when trade flows are not going their way.
Nigeria's unilateral decision to close its border to goods and services from neighbouring Benin and Ghana is a case in point.
Disputes between Uganda and Rwanda, Sudan and Ethiopia, Kenya and Somalia and a protracted row with Egypt over the Grand Ethiopian Renaissance Dam (GERD) being built on the River Nile, are some of the challenges Faki's African Union cannot shy away from as he settles down into his second four-year term as head of the organisation.
Other issues that render his plate full are climate change and terrorism and insecurity in the Sahel.