Chasing 178, England fell short by just one run as they could manage 176/9 in their stipulated quota of 20 overs.
England were cruising towards their target and with 50 needed off 36 balls with eight wickets in hands, the visitors looked all set to cross the line. However, Jason Roy's dismissal sparked South Africa's resurgence.
Even then, Eoin Morgan's 52 meant England needed just seven from the final over, yet Ngidi-who finished with 3/30 -- had Tom Curran caught at deep mid-wicket and bowled Moeen Ali in the final over and prevented the match to go into a Super Over.
For Proteas, Beuran Hendricks who bowled exclusively at the death also played his part with 2/33 in 3 overs while there were also two wickets for Andile Phehlukwayo.
Earlier, England also came out with fantastic death bowling as they restricted South Africa to 177/8. At one stage, the Proteas looked as though they might get a lot closer to 200 after Quinton de Kock and Temba Bavuma put on 48 for the first wicket off only 26 balls and then Bavuma and Rassie van der Dussen a further 63 for the second wicket in 40 balls.
But the England spin duo of Moeen and Rashid slowed things down with returns of 1/22 and 1/23 respectively.
England started off their chase in similar fashion with Roy smashing top score of the match of 70 off 38 balls (7 fours and 3 sixes). Skipper Morgan consolidated for England with the second half-century of the match, but it was his dismissal by Hendricks, preceded by that of Ben Stokes which finally swung the game South Africa's way.
With seven runs required from the final over, Curran managed two off the first ball before getting out. Moeen played and missed before replicating Curran with a quick two before being sent back to the dressing room on the second-last ball of the innings.
Rashid managed to get bat on the final ball, dropping it into mid-wicket, but found the experienced head of Dale Steyn, who under-armed a throw to de Kock to prevent the batsmen completing a second run.
The two teams will now face each other at the Kingsmead, Durban on Friday.
Brief scores: South Africa 177/8 (Temba Bavuma 41, Quinton de Kock 31, Chris Jordan 2/28); England 176/9 (Jason Roy 70, Eoin Morgan 52, Lungi Ngidi 3/30)