The incident at the FNB Stadium occurred at one of the gates, and it is so far unclear what happened.
“We offer our sincere condolences to the family members of those who lost their lives,” Jordaan said in a statement from SAFA on Saturday.
“We are going to ask for a full report and institute a full investigation on what transpired and the cause for the stampede.
“I would also like to wish the injured speedy recovery. A football match is supposed to be a place of entertainment. What happened to at FNB Stadium is very unfortunate,” Jordaan added.
Earlier, the organisers of the pre-season friendly match, Carling Black Label, released a statement sending their condolences
"As sponsors of the Carling Black Label Champion Cup, we are saddened by the fatalities that occurred late this afternoon due to a number of people who attempted to push through the stadium gates," the statement read.
"As things stand at the moment, we can confirm two fatalities caused by blunt force trauma, one critically injured and sixteen spectator with minor injuries.
"This incident is extremely unfortunate as solid security plans were put in place in conjunction with SAPS and various other stake holders, to ensure that this is a risk-free event.
"Since the inception of the Carling Black Label Cup in 2011, we have had record attendance and incident free events.
"The South African Police Services and Stadium Management South Africa are working together to investigate this matter.
"As Carling Black Label, Kaizer Chiefs, Orlando Pirates and SMSA - We wish to express our sincere condolences to the families of those affected by the incident.
"We will endeavour to keep the public informed as we receive progress on the matter."