The Irish full-back gave the Lions a dream start with his try and the tourists were 10 points up in as many minutes as they fought valiantly to square the three-match series.
But, in the end, Morne Steyn's 54-metre penalty with the last kick of the game gave the Springboks a 28-25 victory.
"It's completely gutting to have held onto something for such a large part of the game and to probably have been the better side until that smash right at the end - it's heartbreaking," admitted Kearney.
"Sport can be so cruel and I think we were on the end of the receiving end of that cruelty.
"Sides are always remembered for the final result on the scoreboard regardless of what kind of rugby was played.
"It could have been a very special day for us but the likelihood is it will be remembered with every other Test loss for the Lions."
With Ospreys and Wales full-back Lee Byrne now back home in Wales after damaging his hand, Kearney is guaranteed another start against the World champions.
It could be the second of a possible three appearances for the Louth man against the Springboks, with Peter de Villiers' side also playing Ireland at Croke Park in November.
Kearney said: "I was happy with how I played but I think from 1 to 15 the boys dug really deep and performed really well.
"I suppose that that's what makes things just harder to take.
"When guys are playing out of their skins, and putting in some fantastic performances, to fall just short is heartbreaking.
"We know South Africa play a physical game and probably two of our key guys in the centre (Brian O'Driscoll and Jamie Roberts) took the brunt of that.
"It was unfortunate to lose those guys. But we will pick ourselves up now and a 2-1 defeat would be much better than 3-0."