The match was full of suspense, with the Brazilians saving three match points to draw level in the deciding set, but it ended on a sour note with the referee calling out a Brazilian spike on the fourth match point.
The Brazilians initially contested the call, rushing to the referee and gesturing at him angrily while the Germans had already started their boisterous celebrations. The crowd booed, in a sad end to a tournament that has enthralled Londoners.
Emanuel, a five-time Olympian who had won gold in 2004 and bronze in 2008 with his previous team mate Ricardo Santos, looked dazed as he waited by the podium for the medal ceremony, while first-time Olympian Alison was stony-faced.
But the pair, who are the reigning world champions and were pre-tournament favourites to win gold, began to cheer up once they had their silver medals around their necks, and within a few minutes they were gracious in defeat.
"I'm very happy with this final because it was a great battle. Both teams gave everything to win the gold medal and right now I'm very satisfied because both teams deserved the gold medal," said Emanuel, adding that he had seen a replay of the match point and now accepted that the ball was out.
"(I'm going to) enjoy the silver medal because it's not easy to be in the top in beach volleyball. You saw a lot of good teams passing by in these Games and only three have medals. I'm very satisfied that I have one of them."
For the Germans, it was a huge achievement to break the dual stranglehold of Brazil and the United States over Olympic men's beach volleyball. Since the sport made its Games debut in Atlanta in 1996, US teams had won gold three times while Brazil, in the form of Emanuel and Ricardo, had won once.
"I still can't believe that we really won the Olympic Games.
It's unbelievable and amazing and it will take some days or maybe weeks or maybe months, whatever, to understand what happened here during the past two weeks," said Reckermann.
In a good night for Europe, Latvians Martins Plavins and Janis Smedins won bronze by beating Dutchmen Richard Schuil and Reinder Nummerdor, a surprise result for the Baltic state emerging as an unlikely force in the sport.
The match was tight but in the end youth won out over experience as the Latvians overcame the veteran Dutch pair 19-21 21-19 15-11. Schuil, a five-time Olympian, was part of the Dutch men's indoor volleyball team who won gold in 1996.
"In 2008 Martins was the first Latvian to play beach volleyball in the Olympics, and now it's his second Games and my first. It's just amazing to get third place," said Smedins.
A few minutes after their win, the pair received a congratulatory call from Latvian President Andris Berzins.
The Germans were playing at their second Olympics but it was their first Games together and neither had won a medal before.
Both pairs started out strong in the final, answering each other's powerful attacks and impassable blocks point-for-point throughout the first set.
To the lithe Emanuel's imaginative tactics and the powerful Alison's thunderous spikes, the well-organised Germans responded with dramatic defensive digs and speedy counter-attacks.
The Brazilians obtained a set point at 20-19 but the Germans saved it. The Brazilians went up again to 21-20 but again the Germans denied them. Then it was the Germans' turn to obtain a set point and they nailed it to take the set 23-21.
The first two sets are normally played to 21 points but a two-point advantage is required to win.
The setback appeared to galvanise the Brazilians and the second set followed a very different script.
The massive Alison, 2.03 metres tall and 106 kg, delivered a string of smashes, breaching the German defensive wall again and again, and the Brazilians carved out a comfortable lead to take the set 21-16.
The third set was full of suspense with the teams staying level until the consistent Germans forced Emanuel and Alison into an uncharacteristic string of errors. Brink and Reckermann went up 14-11, giving them three match points, but the Brazilians saved them all.
Then the Germans went ahead again to 15-14, and that was when the close call was made and the match was sealed.
A serene Emanuel did not wish to dwell on the ending but rather on the quality of the play.
"The beach volleyball high level is getting higher and higher ... This is the best thing I can say because I've been playing beach volleyball for 20 years and I saw this sport grow so fast," he said.
"For my country it's good to have one more medal. It's a motivation for the next Olympic Games in Rio de Janeiro. I think every medal will be good for us ... It will motivate the young generation. And I think I did my part."
Asked whether he planned to compete in the 2016 Games, Emanuel smiled, sighed, and said "Rio, Rio, Rio."
He then elaborated on the dilemma.
"It will be my home town but I don't know if I will be in shape until then. I will be 43. I don't think any player has had this challenge. I don't know. I don't have an answer for you right now."