The prince has rarely spoken about his late mother, who died in a car crash in 1997, but the emotion of meeting kids at a social project in a poor area of São Paulo brought memories of her flooding back.
Harry met Cristina da Cruz Nascimento, who is bringing up her granddaughters Karina, 8, and Carolina, 9, because their drug dealer father is in prison and their mother was murdered last year aged 24.
She is also bringing up her great niece Kettelyn, 3, because her mother is a drug addict in São Paulo's infamous Cracolandia –'Crackland'.
Aged 41, she only got a job two months ago as a housekeeper, earning 600 Reals (£160) a month.
She said: "It's really hard with 600 Reals to take care of three children."
Harry said their experiences made him think of the death of his own mother when he was 12.
He told reporters: "There are two little girls – I'm quite emotional – just looking at them I wanted to talk about my own experiences.
"But there is no point because it is just so far removed. The bravery of them looking at me, smiling at me ... I wanted to use my own experiences in a very small way to try to give them a bit of understanding about the fact that I see what you're going through.
"But you hear the stories and think that's nothing to what they have been through."
The Prince said he was close to 'blubbing' after meeting the Brazilian children and their carers.
Harry said: "I was completely overwhelmed and shocked.
"I've never blubbed in public as far as I can remember but I was pretty damn close. It was amazing to hear those stories.
"It seems ridiculous for me to say to these kids how lucky and fortunate they are considering their situation. Obviously they are far from that. But I am only too aware by listening to their stories how many other kids there are like this that aren't as fortunate as them.
"They have been able to be reunited with other members of their families. What this place is doing is reuniting children as young as eight years old.
"One of these kids here was five days old – born at eight months – when he was left on the street by his mother because she was on crack."
The prince was visiting Acer, a project run by a Briton, Jonathan Hannay, to help underprivileged children in Diadema, São Paulo.
One of its projects is to help children with no parents by reuniting them with members of their extended family.