A brilliant touchline conversion with the last kick of the game prevented the Lions from getting back to winning ways in Cape Town.
The tourists were leading 13-6 in a hard-fought match when replacement Emerging Springboks wing Danwel Demas went over in the corner for a try.
Willem de Waal then kept his nerve to slot his kick from the right-hand touchline, ending the Lions' hopes of a 100% record in the non-Test matches and preventing them from regaining momentum after Saturday's 26-21 defeat in the first Test.
A sharply-taken try in the first half by Keith Earls had been the difference between the sides before the dramatic conclusion.
The home side might even have clinched the win, had it not been for fly-half Earl Rose missing kickable penalties either side of the interval.
Chances were at a premium at Newlands because of the heavy rain and sodden pitch and few of the Lions were able to stake a claim for inclusion in the second Test.
Luke Fitzgerald was a notable exception, proving sharp in attack and solid in defence.
And there were a few jinking cameos from his fellow winger Shane Williams, but perhaps not enough to force his way into the side for the trip to Pretoria.
The other main contender for a Test place, Martyn Williams, looked to be struggling with a knee problem.
Head coach Ian McGeechan had said he expected the Emerging Boks to be his side's toughest opposition of the warm-up games and they remained in contention to the end.
Man-of-the-match Jean Deysel and skipper Dewald Potgieter were at the heart of an impressive display.
The Lions tried to run the ball whenever possible, despite the heavy showers and strong winds in Cape Town.
Williams and Fitzgerald both produced sharp breaks early on, with the Emerging Boks seemingly unnerved by the Lions' aggressive blitz defence as they struggled to play the fluent game promised by their coach Dick Muir.
Zane Kirchner's misguided clearance kick went straight to Martyn Williams, and his offload found centre Riki Flutey, who set off towards the try-line before being hauled down.
Earls soon capitalised though, stepping cleverly off his left foot to fool Jano Vermaak and go in under the posts.
After his nightmare display against the Royal XV in the opening game of the tour, the young Irish full-back has done himself great credit with his pace and footwork.
Earls defied the conditions to score a fine first-half try
The second half was as tight and attritional as the first, dominated by kicking and lost possession.
James Hook looked to have sealed victory for the tourists when he slotted a penalty three minutes from time.
However, with a minute left the Emerging Boks kicked a penalty to the corner and won the resulting line-out.
The Lions bravely resisted the drive, but ran out of numbers and Heini Adams passed to Demas, who went over in the corner.
De Waal faced a devilishly difficult kick in the corner, but held his nerve to score from 30 metres out on the touchline.
Emerging Springboks: Zane Kirchner, Luzuko Vulindlu, Deon van Rensburg, Morgan Newman, Bjorn Basson, Earl Rose, Jano Vermaak; Wian du Preez, Bandise Maku, Werner Kruger, Steven Sykes, Wilheim Steenkamp, Dewald, Potgieter (capt), Jean Deysel, Duane Vermeulen.
Replacements: Tiaan Liebenberg (for Maku, 52), Pat Cilliers (for Du Preez, 64), Franco van der Merwe (for Sykes, 64), Jacques Botes (for Deysel, 64), Heini Adams (for Vermaak, 64), Willem de Waal (for Van Rensbug, 52), Danwel Demas for Basson, 73).
Lions: Keith Earls, Shane Williams, Riki Flutey, Gordon D'Arcy, Luke Fitzgerald; Ronan O'Gara (capt), Harry Ellis; Tim Payne, Ross Ford, John Hayes, Donncha O'Callaghan, Nathan Hines, Joe Worsley, Martyn Williams, Andy Powell.
Replacements: Lee Mears (for Ford, 75), Phil Vickery (for Hayes, 67), Simon Shaw (for Hines, 57), David Wallace (for Powell, 68), James Hook (for O'Gara, 45), Ugo Monye (for Fitzgerald, 65). Not used: Mike Blair
Referee: Alain Rolland (Ireland)