Just when it seemed that the teams were headed for their third successive draw, Franklyn Cale flashed through a huge gap in the Santos back line to score the only goal of the match past Brenden Wardle who, in his usual fashion, had rushed out of his goal.
Santos created the better openings, but rotten shooting technique all round saw it go to waste.
Ajax came more into the game in the latter stages, but were also found wanting in the finishing stakes, with a number of goalmouth scrambles producing nothing.
Winning coach Gordon Igesund pulled out an ace at the last minute by fielding experienced goalkeeper Moeneeb Josephs when everyone, including Santos, were expecting to face young Andre Petim.
Josephs was only due back in a month's time, but somehow made a miraculous recovery from a serious ankle injury.
It proved a timely comeback as the Bafana Bafana hopeful commanded his area with aplomb.
The agile keeper, who joined a long list of players to captain the Urban Warriors, was soon in the thick of things as Roger da Sa's team probed with intent from the outset.
A bouncing effort from some distance by Marawaan Bantam almost caught out Josephs, who responded with an unorthodox dive to keep his goal intact.
The play of the match should have resulted in the opening goal, but Santos's culprit-in-chief, Carlo Scott, put clear with a great pass from Bantam, fluffed his lines with only Josephs to beat.
Stanton Lewis of Ajax had the next opportunity, but he too sent a shot wide from close range when it looked easier to hit the target.
In copycat fashion, Santos skipper Musa Otieno later headed Rueben Cloete's superb free-kick over the bar with Josephs and his defence nowhere.
Later still, Thembile Kanono selfishly shot at goal with his weaker left foot when hot shot Cloete should have been the recipient of a slide-rule pass inside the box.
And even before local referee Jerome Damon blew for halftime, Cloete hit the side net from close range and Scott's first touch again let him down when he had raced clear of the defence.
It was more of the same after the break, but Scott will probably not be keen to see a replay of his miss after 58 minutes.
A bit of ping-pong with younger brother Romano saw the ball drop into space behind the Ajax back line.
Scott ran in unchallenged but, to the dismay of the Santos bench and fans, his shot from inside the small box almost hit the corner flag.
Igesund brought on Terror Fanteni for Lewis, but nothing much materialised for the lively striker as Ajax were not enjoying one of their more creative outings.
Wardle dealt well with the high balls Ajax sent his way.
For the rest, the derby lived up to its billing as a fierce battle for Cape football turf.
Damon flashed two yellow cards per team in the first stanza - on top of allowing a couple of hard tackles to go unpunished, no doubt in the spirit of the occasion.