Costa, 31, pleaded guilty in a Madrid court on Thursday morning to evading €1.1 million in taxes on his image rights.
Costa paid tax authorities the outstanding amount in full last year and will pay the €543,208 penalty on top of that.
His prison sentence has been replaced by an additional fine, as is customary in Spain for jail terms of under two years.
"Diego Costa reached an agreement a few months ago with the prosecutor and has already paid the corresponding fine plus interest and the request for a prison sentence was withdrawn," an Atletico spokesman told Reuters on Wednesday.
"This week it is expected that an agreement will be ratified in court, as is mandatory."
The striker is the latest player to fall foul of Spanish authorities over tax evasion on image rights, with a number of high-profile cases in recent years.
In January 2019, Cristiano Ronaldo agreed to hand over a total of €18.8m in fines and taxes and was given a 23-month sentence, substituted for another €365,000 payment.
Xabi Alonso, one of the few players to fight charges after refusing to strike a deal, was acquitted of tax fraud last November, although prosecutors have appealed.
Information from Reuters was used in this report.