Barca deposited the money with a notary as they waited to see whether his move to Paris Saint-Germain would go through.
Following the completion of his world record €222m switch, Barca spokesman Josep Vives said the bonus would not be paid as "the agreed conditions have not been met."
Barca made an initial payment -- reported to be around €14m -- when the five-year deal was signed, and had been due to make the second payment on Sept. 1.
But Vives said: "There were three conditions -- one, that the player didn't negotiate with another club before July 31; two, that he publicly expressed his decision to fulfil his contract; and three, the payment was to be made on Sep. 1 to ensure he didn't go to another club.
"With these criteria not met, the club will not pay the renewal bonus. The money is no longer with a notary but back with the club."
Meanwhile FIFPro, the worldwide representative organisation for all professional footballers, has called for an investigation into the increasing cost of transfers in European football.
It is concerned that an inflated and distorted market is contributing to the destruction of competitive balance.
General secretary Theo van Seggelen has urged the European Commission to undergo an urgent review of transfer rules which have been in place since 2001.
In a statement, he said: "FIFPro is calling on the commission to investigate the flow of money via transfer fees within the European Union territory to understand their impact on competitive balance in the region.
"The world-record transfer of Neymar is the latest example of how football is ever more the domain of a select group of rich, mostly European-based clubs.
"Given that much of football's financial activity occurs within Europe, where significant transfer fees are exchanged between clubs, FIFPro is asking the European Commission to launch of thorough investigation of the transfer rules it approved in 2001 and which are now in need of urgent review."
Van Seggelen voiced concern that "football's enormous wealth is trapped within a few leagues and clubs when it could be redistributed more efficiently and fairly to help protect competitive balance."
Later on Friday, Neymar Sr. spoke about Barca's refusal to pay, telling Cadena Cope: "If Barca doesn't pay us, there is nothing I can do.
"Now it's too late to negotiate. ... And Barcelona no longer have my support. I was on Barca's side trying to convince Neymar to stay. But with this attitude from the team's front office I can't be on its side anymore because the agreement is specific and very clear.
"It's a clause about the signing of a new contract, and that's the reason why the team increased the value of buyout clause. ... This is something we'll need to review and discuss in the future, now is not the right moment.
"FC Barcelona has to do what they think is right for them. But I know what we talked and I can look into the eyes of everybody. I was there and I know what we agreed to do."
Speaking earlier this week, La Liga president Javier Tebas accused PSG of "financial doping" and said he would complain to both UEFA and the EU.
Last week, Barcelona sources said the club would put pressure on UEFA to investigate how PSG were financing the Neymar move.
However, UEFA said in a statement that it "has not received complaints from anyone regarding this matter" and added that officials would examine the deal to ensure it complies with financial fair play regulations.