FA general secretary Alex Horne said the sanctions did not send a "strong enough message" about racism, and that the governing body will appeal against two-match and one-match bans for Steven Caulker and Tom Ince respectively.
Rio and Anton Ferdinand also criticised the sanctions on Twitter contrasting it with a 100,000 euro and one-match ban handed to former Arsenal striker Nicklas Bendtner for displaying a betting firm's logo on his underpants during Euro 2012. Horne said: "We are disappointed with the sanctions levied by UEFA with regards to the racist behaviour displayed towards England's players."
UEFA's control and disciplinary body also banned four Serbian players and two coaches for varying terms after ugly scenes marred the end of the European Championship play-off in Krusevac in October.
Horne added: "Let's be clear, racism is unacceptable in any form, and should play no part in football. The scenes were deplorable and we do not believe the sanction sends a strong enough message."
Anton Ferdinand tweeted: "Wow UEFA ain't serious with their punishment... So showin a sponsor is worst than racism and fighting!"
His brother Rio added: "Uefa are not serious at all on racism. Fines do not work at all. They have zero impact on federations/clubs/fans/players £fact. Uefa need to talk to this generation.....they don't seem to be up to date on this issue?? Harsh punishments needed as a deterrent £simple."
Sports minister Hugh Robertson, who had written to UEFA president Michel Platini demanding tough action for the racist abuse, also expressed his disappointment.
Robertson said: "I am disappointed in the punishment that has been handed to the Serbian FA given the widespread racist abuse that England's Under-21 team suffered that night. Racism is completely unacceptable and we need tough sanctions to help combat it."
The FA had reported the racist abuse to UEFA plus a number of other incidents. Full-back Danny Rose, who was dismissed after the final whistle for kicking the ball away in anger, complained he had been subjected to monkey chants throughout the match and as he left the pitch.
The Serbian FA had denied the racism charges and said after the match that Tottenham Hotspur defender Rose, who is on loan at Sunderland, had provoked the home fans in an "inappropriate, unsportsmanlike and vulgar manner".
Serbia have long since had problems with racism and football violence.
They were forced to play a Euro 2012 qualifier behind closed doors after fans rioted and caused a senior international game against Italy to be abandoned in Genoa in 2010.
In June 2007, the FSS was fined £16,500 because of racist chants and the behaviour of their fans at another under-21 match against England.
FSS secretary general Zoran Lakovic appeared to agree his organisation had got off lightly following this latest incident.
"The punishment is not as harsh as we thought it might be but the verdict and the incident that caused it should come as a last warning to everyone representing Serbian football," Lakovic said.
"That means the coaches, the players and of course the fans because even the slightest trouble in future could result in the most rigorous measures."
The fine of 80,000 euros is 20,000 less than UEFA fined Denmark striker Nicklas Bendtner at Euro 2012 for showing the logo of a betting company on his underpants while celebrating a goal.
England players involved in the post-match fighting in October were also punished by UEFA.
Defender Steven Caulker, who plays for Tottenham, was suspended for two international matches and Blackpool winger Tom Ince for one.
The sanctions provoked a frustrated response from England under-21 coach Stuart Pearce.
"I am concerned to see our players suspended by UEFA and we will continue to support them," Pearce said.
"I maintain our players played no part in the aggression. From what I witnessed our players and staff were forced to protect themselves in the violent scenes that followed the game."