Two members of Togo's national football delegation died on Saturday following an ambush on Friday, a team member told French radio.
The attack, in which the driver was killed and seven injured, took place in Cabinda, a province where guerrillas have fought a secession campaign for decades.
"It has no impact on our World Cup," Jordaan told Reuters from Luanda where he is to act as match commissioner for Sunday's Nations Cup opener between Angola and Mali.
"The world understands that sovereign countries are responsible for their own safety and security and to say what happened in Angola impacts on the World Cup in South Africa is the same as suggesting that when a bomb goes off in Spain, it threatens London's ability to host the next Olympics.
"It is nonsensical for South Africa to be tainted with what happens in Angola, which is not even one of our neighbouring countries."
Jordaan said the bus attack was a blow for Nations Cup hosts Angola.
"I feel very sorry for the Angolans because they have spent billions on fixing up their cities and building infrastructure for this tournament. This was going to be the event that would mark their transition from decades of war to a new social and economic order. In that context, it's a blow."
Former African Footballer of the Year and president of Zambia's football association Kalusha Bwalya said the attack was a huge setback for African football.
"It's a very negative blow for Africa and our football," he said.
"It's really disturbing that something like this has happened in the months leading up to the World Cup."
Former Togo coach Otto Pfister said there was no need for panic.
"The shocking attack in Angola will be projected on to the World Cup in South Africa," said German Pfister, who has taken charge of eight different African national teams.
"It is a big blow for Africa because it will give the critics more fuel. But you cannot compare Angola with South Africa and there is no need for panic."
Violence erupted in north Africa two months ago when Egypt and Algeria met in two crucial World Cup qualifiers.
Algeria had their team bus stoned by Egyptian fans in Cairo while businesses with Egyptian connections were burnt and looted in retaliation in Algiers.
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