The Lions refused the chance of an easy three points and a draw when they trailed late on, going for a quick tap restart from which Van der Merwe barged over the line to seal a third successive win for the home side.
Prior to that the match had been a kicking dual between Bulls flyhalf Jacques-Louis Potgieter and his opposite number Elton Jantjies.
The home side had moved into a 6-0 lead inside the first 20 minutes through two Jantjies penalties, but Potgieter landed three of his own to give the visitors a 9-6 halftime advantage.
The see-saw battle continued as Jantjies land two more penalties to put the Lions ahead, before the Bulls struck back as two Potgieter kicks edged them in front once more.
Jantjies levelled the scores again but the Bulls looked to have grabbed victory when Potgieter put them ahead with two minutes remaining on the clock.
But brave captaincy saw the Lions go for the win and their ambition paid dividends.
Two points now separate the top four teams in the South African conference with the Bulls in pole position, just ahead of the Sharks, Stormers and Lions.
(Reporting by Nick Said, editing by Ed Osmond)
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