A Stanley Ohawuchi goal on 64 minutes was not enough for the home team as they trailed by three goals from the first leg.
Mamelodi Sundowns of South Africa won a fairytale first CAF Champions League title on Sunday despite a 1-0 second-leg loss to Zamalek of Egypt in Alexandria.
A Stanley Ohawuchi goal on 64 minutes was not enough for the home team as they trailed by three goals from the first leg in Pretoria last weekend and lost 3-1 on aggregate.
It was a remarkable triumph because the South Africans were eliminated in the final qualifying round in April only to be reinstated when their Democratic Republic of Congo opponents were disqualified.
Success for Sundowns made them $1.5 million (1.38 million euros) richer and secured a place at the FIFA Club World Cup in Japan during December.
"It was an amazing journey of ups and downs and now we are the champions of Africa," said Sundowns' Zimbabwe striker Khama Billiat.
"We look forward to Japan and facing the best clubs in the game. It is going to be an absolute pleasure."
Winger Keagan Dolly said: "We knew it was going to be difficult because Zamalek are a great team with some outstanding individuals.
"Some people will say we were lucky to get a second chance after being eliminated, but I believe we deserve to be African champions."
Goalkeeper Ahmed El Shenawy and captain and midfielder "Shikabala" were among those dropped as Zamalek coach Moamen Soliman made four changes from the side that started the first leg.
Sundowns coach Pitso Mosimane had to make one enforced alteration with huge Ivorian centre-back Bangaly Soumahoro coming in for suspended Wayne Arendse.
Although facing a mammoth task, history offered a hope to Zamalek with two of three previous Champions League finalists in a similar predicament emerging as overall winners.
An estimated 60,000 predominantly Zamalek supporters were inside the 86,000-capacity Borg El Arab Stadium on the outskirts of Alexandria as the match kicked off.
There are few more nerve-inducing factors in African football than a large Egyptian crowd roaring on their team, but Sundowns calmly survived early pressure.
The first scoring chance for the hosts came after 12 minutes when Nigerian Ohawuchi burst through and beat goalkeeper Dennis Onyango, but the ball trickled wide.
Ugandan Onyango, a 2016 Africa-based Footballer of the Year finalist, needed medical attention three times before being replaced by Wayne Sandilands on 28 minutes.
Striker Basem Morsy had been headlined as the Zamalek dangerman, but recent signing Ohawuchi was posing a bigger threat.
A wild but crucial clearance from Soumahoro foiled another attempt by the Nigerian to break the deadlock before Sundowns began to threaten going forward.
The first serious chance for the South Africans came on 35 minutes when awarded a free-kick just outside the box, but captain Hlompho Kekana struck the ball into the wall.
Zamalek goalkeeper Mahmoud Abdel Rahim did well to push away a goal-bound shot from Percy Tau and a looping Billiat shot struck the top of the crossbar before flying wide.
The injuries to Onyango meant eight minutes of first-half stoppage time during which Liberian Anthony Laffor troubled Zamalek twice with a shot and a header.
Half-time arrived with the second leg goalless and Sundowns retaining the three-goal advantage they established in Pretoria last weekend.
Zamalek started the second half as they did the first, controlling possession and territory but rarely looking like cracking open Sundowns' defence.
After 64 minutes the Egyptian outfit scored and it was no surprise that the goal came from livewire Ohawuchi.
Receiving possession well outside the box, he beat one man and unleashed a low, long-range drive that flew into the corner of the net off the left hand of Sandilands.