Wayne Parnell prevented Pakistan's tail from getting 10 off the final over of their second Twenty20 international to secure South Africa victory in Dubai and a series clean sweep.
The Proteas had won the previous match by nine wickets, but this encounter went down to the wire as Pakistan attempted to chase down their total of 150.
Touring captain Faf du Plessis top scored for South Africa and put on 82 with Hashim Amla for the second wicket partnership, which capitalised on the rapid start provided by Quinton de Kock.
He smashed four boundaries in a 19-ball 30 before falling to Saeed Ajmal, who had Amla caught by Shoaib Malik for 48 in the 15th over on his way to figures of 3-25.
Du Plessis kicked on to end unbeaten on 58, but a couple of wickets for Sohail Tanvir and another for Ajmal gave Pakistan some momentum at the back end of the South Africa innings.
Their batsmen seemed to build on this by reaching 39-0 after five overs, but two wickets in two balls from Parnell saw Ahmed Shehzad [21] and Mohammad Hafeez [0] back in the pavilion.
Sohaib Maqsood hit a well-paced 37, and with support from Malik [15] and Umar Akmal [11], he helped put Pakistan in a winning position at 112-4, but they then lost three wickets without adding to the scores.
Things were left to numbers 10 and 11, Ajmal and Mohammad Irfan, to try to get the Asian nation over the line, but Parnell kept things tight in the final over to earn South Africa a six-run win.
