Evan Jones had brought the Lions back into the game from the depths of a loss, smashing 54 from just 18 balls as the home team tried to chase down a target of 182.
The Lions then needed one run from two balls to win the match but Ruan de Swardt took the wickets of Mitchell van Buuren and Wandile Makwetu as the encounter ended in a tie.
De Swardt then also bowled the super over and limited the hosts to eight runs and getting the crucial wicket of Jones.
Lesiba Ngoepe then hit two fours before visiting skipper Wihan Lubbe secured the final run that meant the Dragons had only won their second T20 match out of seven this campaign.
The Lions have no victories from five games and last season's champions cannot reach the playoffs with two matches remaining.
The Dragons had earlier posted a total of 181-6 in their 20 overs after being put in to bat at the toss.
Janneman Malan top-scored with 56 from 43 deliveries but the innings was given impetus at the back-end when De Swardt smashed an unbeaten 45 off just 20 balls.
The Lions next face Western Province at Newlands on Friday before ending their CSA T20 Challenge campaign against the Dolphins in Durban on Sunday.
The Dafabet Warriors stormed to the top of the CSA T20 Challenge log on Wednesday night, hammering previously unbeaten Goldrush Boland by 98 runs and securing a bonus point in the process.
The CSA T20 Challenge clash between the Titans and Lions at SuperSport Park in Centurion ended without a ball being bowled after relentless rain on Sunday forced the match to be called off.
The Warriors secured their spot in the CSA T20 Challenge playoffs after a convincing 54-run victory against the Tuskers in Pietermaritzburg on Saturday.
Boland preserved their perfect start to the CSA T20 Challenge with a nerve-shredding five-run victory over the Dolphins in Paarl on Friday evening.
