Aubameyang used social media to highlight their plight after arriving at Banjul airport on Sunday, ahead of Monday's Group D clash in the Gambian capital.
The Gabon delegation were told they were not allowed to leave the airport because of an administrative problem and were forced to sleep on the floor before being allowed to leave in the morning after government intervention.
.@Aubameyang7 and his Gabon teammates were stuck at the airport in Gambia for over six hours after landing for an Africa Cup of Nations qualifier.— ESPN FC (@ESPNFC) November 16, 2020
They eventually left at 6am, just 10 hours before kick off 😴 pic.twitter.com/0ZJpulM0qQ
No reason was given for not allowing the team to exit the airport and head to their hotel after arrival. Gabon's federation posted pictures of the incident on its Facebook page but without any comment.
Aubameyang posted on Twitter in a reference to previous foibles blamed on the Confederation of African Football: "Nice job CAF, it's as if we were back in the 1990s.
"This will not demotivate us but people need to know and CAF need to take responsibility," he added later. "[It is] 2020 and we want Africa to grow but this is not how we will get there."
However, Gambia head coach Tom Saintfiet has told ESPN that Gabon have been the engineers of their own plight after refusing to take COVID-19 tests upon their arrival.
"Gabon refused to be tested," he said. "They arrived last night at 11.30 p.m. at night in Gambia, they refused to be tested in the airport.
"That's the reason they stayed so long there, and then in the hotel they refused to be tested. The FIFA and CAF rules are clear; you have to be tested in the host country 24 hours before the match.
"When we went to Gabon, we were tested in Gabon in the airport and the hotel. We were twice tested there, even if we had certificates from Europe, in Africa, upon our arrival, that we are negative.
"They were refusing to play. If CAF had accepted this, it would have been a scandal to the hilt and a pandemic risk, because players can infect others, they can get sick, even die, and maybe in the future, clubs will refuse to release players as they return sick.
"It's not possible, and is irresponsible to play this game without having tested players upon arrival in this country."
Gabon are top of the group standings, three points ahead of Gambia, who are seeking to reach the Nations Cup finals for the first time.
Before the match, Aubameyang said that Gabon were even more determined to get a result after sleeping at the airport.
"No matter the result for me my team won already when I see the faces this morning everyone is hungry hungry about football."
ESPN have approached Gabon FA President Pierre Alain Mounguengui for further comment.
Information from ESPN's Ed Dove has been included in this report.