Officials from the two countries stressed this at a memorial service for Macia in Daveyton on Wednesday.
"People in Mozambique have responded in the same way the majority of South Africans have; they were shocked – and we're still shocked," said Mozambique ambassador to South Africa Fernando Fazenda.
"However, if you went back to history, you would see that Mozambique was … liberated before South Africa. Samora Machel used to say: 'Before South Africa is liberated, our liberation is meaningless'. This is the message that is still prevalent today. eMido, like many other Mozambicans, regarded South Africa as his second home."
The sentiments were repeated by ANC secretary general Gwede Mantashe, who arrived at the tail-end of the event, and said: "Our relationship with the people of Mozambique is deep. They paid a heavy price for our freedom. We owe it to them. This incident is ugly. The last time we saw it done was done by a farmer. We were outraged then and we are outraged now."
Mantashe added that more than diplomatic ties, incidents such as these have the potential of affecting people to people relationships, as South Africa's "growing tendency for violence" was being deeply felt in its communities.
The possible consequences of Macia's violent death that has left devastated communities on the ground rather than shaking up the corridors of power, was echoed by a Macia family friend Lawrence Mabaso, who said: "The situation in the communities is not good. People are feeling unsafe and vulnerable and some are even considering going home. The police, it seems are out of control."
Mabaso said while Macia's family had welcomed the Ekurhuleni Metropolitan Municipality's gesture to contribute towards the funeral costs, it would not heal the hurt the family was currently experiencing.
Former South African first lady and former wife of assassinated Mozambican president Samora Machel, Graça Machel, said the tendencies for South African violence stemmed from not knowing how to heal the wounds of its past.
"We expect the police to protect people so it's clear we have a lot of problems. We have to find a way of dealing with our emotions. We are holding hands but as a society we are grieving and we are in pain and we don't know how to deal with it," she said.
Provincial and local police representatives were asked to leave by an angry crowd that voiced its displeasure at their uniformed presence.
Macia's memorial, ironically, took place on National Police Day.
The memorial, attended by several provincial politicians and many taxi bosses, was marked by a strong anti-police sentiment, with Gauteng minister for community safety Faith Mazibuko only barely being allowed to speak.
Macia will be buried on Saturday, in Matola, south of Maputo. Matola, where about a dozen South African political activists were killed in a raid by the apartheid government, remains a symbol of the two countries' ties in the fight to end repressive regimes.