Al Ahli won 3-1 on aggregate after a 1-1 draw in the first leg in Soweto last weekend.
Al Ahli's Mohamed Aboutrika underlined his status as the most successful player in African club competition by scoring.
His 54th minute strike set up the Egyptians for their second-leg victory over the South Africans in Cairo, and a 3-1 aggregate triumph, to put a successful seal on a stellar career.
Ahmed Abdelzaher added a second goal 12 minutes from time to ensure Ahli lifted the trophy for a record-extending eighth time, after a 1-1 draw in the first leg in Soweto last weekend, and qualified for next month's Club World Cup in Morocco.
Egyptian Aboutrika, playing his last home game before retiring at the end of the year, has featured in five of Al Ahli's Champions League-winning sides in the last eight years, consistently delivering talismanic performances.
He swept home a loose ball from close range after a shot from Ahmed Fathi was blocked by the Pirates defence but fell fortuitously into his path, underlining Aboutrika's uncanny ability to pop up in the right place at the right time.
The goal came at a crucial time for Ahli, who had spent most of the game on the back foot before breaking the spirit of the South Africans and allowing the Cairo club to assume command.
The Egyptian side's success came against a backdrop of political upheaval in the north African country, which has had a major impact on Ahli who have not played outside the Champions League since the domestic league was cancelled in June.
It was only a special concession by the country's military authorities that allowed the final to be played in Cairo, where all major football had been stopped since the overthrow of president Mohamed Mursi's government in July.
Some 30,000 spectators were allowed into the Arab Contractors Stadium, with clashes reported outside between police and ticketless supporters seeking entry.
It was a rare opportunity for Ahli to play in front of a home crowd but they were kept mostly quiet in the first half as Tlou Segolela missed two good chances to give Pirates the lead.
Pirates striker Lennox Bacela went round the keeper soon after Aboutrika's goal but somehow missed the target before the unmarked Abdelzaher swept the ball home for Ahli's second goal.
Aboutrika, who has also won three African Nations Cup titles with Egypt, was substituted to an emotional send off in stoppage time, swamped by the collective embrace of his bench, policemen and photographers as he left the field in triumph.
- Sports & Recreation
- Mohamed Aboutrika