Thursday's game saw home fans pelting Ghana's players and supporters with bottles, rocks, broken glass and cutlery after Equatorial Guinea conceded two quick first half goals.
The game resumed in the second half but was halted after further violence directed at Ghana's supporters.
According to eye witnesses the security situation was sufficiently dire that a helicopter was deployed to hover low over the stadium and scatter the rioting fans.
There were reports of further riots in the streets around the stadium. Several Ghanaian supporters were also injured during the violence. One Ghanaian football official described the scene as being like a "warzone."
"In front of me was utter chaos -- angry, screaming fans. But there were scared, scurrying fans, too," recalled Gary Al Smith, a Ghanaian football journalist who was in the stadium at the time.
"I've never played in front of anything like that and I'd like to say sorry on behalf of my team," said Equatorial Guinea's star player Emilio Nsue after the match was restarted and his team had lost 3-0.
"It was an odd experience -- one I've never felt before."
Yet on the eve of the final, Blatter and Hayatou held a join press conference where the Cameroonian blamed western journalists for making the violence sound worse than it was.
"When something bad happens in Europe, they say it's an error. When something happens in Africa, they begin talking about corruption," Hayatou said, before adding that he believed "the western media are simply here to perpetuate colonization."
Blatter, who will fight a FIFA presidential election in May and is relying on African votes to secure another term of office, later spoke about the general state of football in Africa and how the western world covers it.
The Swiss said he wanted more good news stories.
"I don't see the negative side of African football that the media presents," said Blatter.
"The media can play a role, must play a role, but they must play a role where the notions of respect and fair play are the basics.
"Today the world opens the newspapers, watches television, and sees only murders and killing," he added.
"We never talk about princesses marrying any more."
Blatter went on to congratulate Equatorial Guinea's hosting of the tournament. The tiny oil rich nation, which has been severely criticized over its human rights record, stepped in at the last moment after Morocco pulled out citing fears about the spread of the Ebola virus.
Equatorial Guinea had been fined close to $100,000 over the violence and ordered to pay the expenses of the 36 injured Ghanaian fans.
Saturday saw another potential flashpoint pass without incident.
The Democratic Republic of Congo beat Equatorial Guinea on penalties in the third place play off after the two teams played out a 0-0 draw.
Before the game several players had suggested that the tie should be played behind closed doors with no supporters.
One player, Democratic Republic of Congo defender Gabriel Zakuani, even suggested forfeiting the match altogether.
"If they're throwing this at players, Eq Guinea, you can have 3rd place," he tweeted after the incident, alongside a picture of some of the objects that had been thrown from the stands.
"I love football but prefer to live. #AFCON2015."
In the end the match took place under tight security with barely 500 supporters in the stadium. All eyes will now be on Sunday's showpiece final, which will again take place in Bata.
Meanwhile, journalists covering the event have reacted incredulously to Hayatou and Blatter's remarks.
"Blatter's got me bang to rights," tweeted British football journalist Jonathan Wilson.
"I for one am ashamed I reported the trouble I witnessed in Malabo rather than seeking a marrying princess."