The 'dreadlocked destroyer' showed tantalizing glimpses of the form which had seen him dispatch Nadal in a dramatic style Thursday, but could not put Troicki under any sustained pressure, despite winning the third set.
Troicki, moving up the world rankings after a controversial doping ban, seized his opportunities at key moments in the match played before a packed and expectant Court Three crowd to win 6-4 7-6 4-6 6-3.
Brown, who captured the imagination of tennis fans around the world with his audacious net-charging play against Nadal, gave his new followers renewed hope when he broke Troicki's metronomic service for the first time to force a fourth set.
But the 22nd seed Troicki was not in the mood to throw away his advantage and an early break put Brown on the back foot.
The match ended in tame fashion when Brown double faulted on Troicki's second match point, in many ways encapsulating the maverick nature of his play.
Consolation will come in the form of the biggest check of his career, £75,000 ($120,000) for reaching the third round of the most lucrative grand slam event in the world.
"Obviously it's great to make money in a tournament like this. But people don't look at the bunch of weeks where the first round of challenger in Italy, for example, you get 300 euros minus 30 percent tax. You can check what a flight is from Frankfurt to Italy," said Brown after his exit.
The 30-year-old, who has a Jamaican father and German mother, has spent most of his career on the second tier ATP Challenger circuit, but had a previous win over Nadal at Halle and has also a beaten Lleyton Hewitt at Wimbledon.
Home hope out
Troicki, a Davis Cup teammate of defending champion Novak Djokovic, will next face Canada's Vasek Pospisil for a place in the last eight. Pospisil put out home home James Ward in a later five-set thriller.
Nadal's departure removed the 14-time grand slam champion from the side of the draw occupied by Roger Federer and Britain's Andy Murray and both were in third round action Saturday.
Federer tamed the massive serving of ruggedly built Australian Sam Groth, who had the Centre Court crowd gasping with the power of his delivery.
One effort topped out at 147mph (225kph) just shy of the Wimbledon record held by American Taylor Dent, but for all his belligerence, Groth could not match the all round excellence of seven-time champion Federer.
The second seed looked set for a straight sets win until Groth took advantage of a rare slip up in the third set tiebreaker by Federer to pull a set back.
But two breaks of service in the fourth set put the Swiss maestro into the second week with a 6-4 6-4 6-7 6-2 in two hours 16 minutes.
Karlovic upsets Tsonga
But there were upsets as Croatia's Ivo Karlovic beat French 13th seed Jo-Wilfried Tsonga.
The 36-year-old veteran, who can match the service power of Groth, fired 41 aces in a 7-6 4-6 7-6 7-6 third round victory.
"It's a great feeling, you know. I really like what I do. I'm just having fun. So if I'm able to do this at my age, it is unbelievable still," he said.
Karlovic has earned a last 16 clash with Murray, who had to survive a scare of his own before beating Andrea Seppi of Italy in four sets.
Murray, the 2013 champion, required a medical time-out for treatment on his right shoulder after dropping the first game of the fourth set.
But the third seed was able to shrug off the injury and took the next six games to win 6-2 6-2 1-6 6-1 to the relief of the home crowd.
After this match, there was a late night treat for spectators as the Centre Court roof was closed to allow Gilles Simon to complete a five-set victory over fellow Frenchman Gael Monfils.
Simon was pegged back to two sets all, but broke early in the fifth to complete a 3-6 6-3 7-6 2-6 6-2 victory in a match that had started on Court One.
He will play the Czech sixth seed Tomas Berdych for a place in the last eight.
Champion Kvitova out
The women's singles provided the shock of the day as defending champion Petra Kvitova went out in three sets to Serbian Jelena Jankovic.
The second seed looked in command when she led by a set and 4-2 before Jankovic hit back to level and won the decider for a 3-6 7-5 6-4 victory.
It earned the 28th seed a fourth round match against Agnieszka Radwanska, who beat Australain Casey Dellacqua in straight sets, but was unexpected given her recent form and injuries.
"it's a really big win for me, especially playing on Centre Court against a two‑time champion, Wimbledon champion. It's really amazing," she said.
"I was just happy to be playing and competing on grass. Grass is not my favorite surface. And Petra plays so well on it. I think it's her favorite surface. It shows by winning two Wimbledon titles."
A shocked Kvitova said she would be taking some time off after a devastating reverse which was unexpected given her early dominance in the match.
'"I'm not really sure what happened out there. I was kind of up in the second set. Suddenly I felt like she's, you know, coming back, playing a little bit aggressive.
"Suddenly from my side, I didn't have answer for it. My serve didn't help me at all this time, as well. I was really struggling with each shot which I played."
Wimbledon specialist Sabine Lisicki also went out to Tmea Bacsinszky of Switzerland in straight sets, but Denmark's Caroline Woznniaki and Madison Keys of the United States made the last 16.