The 56-year-old is accused of committing tax fraud in 2011 and 2012 when he coached Spanish giants Real Madrid.
According to the agreement seen by AFP, Mourinho accepted a one-year jail sentence immediately commuted to a fine of 182,500 euros.
The Portuguese coach will also have to pay an additional penalty of €1.98 million ($2.3 million).
Mourinho already paid €1.14 million in 2015 as an administrative penalty and the deal stipulates thatprosecutors won't oppose that this amount be deduced from the overall fine.
The agreement still has to be validated by a judge.
Mourinho, sacked by Manchester United in December following a string of disappointing performances, is the latest high-profile football figure to be judged over his tax affairs in Spain.
Spanish prosecutors accuse Mourinho, who coached Real Madrid between 2010 and 2013, of failing to declare income of €1.6 million in 2011 and €1.7 million in 2012.
The grounds for the case, as with a series of others involving football stars based in Spain, is how income from Mourinho's image rights was managed and declared.
Prosecutors believe by ceding his image rights to a series of companies based in tax havens, Mourinho committed fraud by not declaring the income those companies made from the rights.
Cristiano Ronaldo, now of Juventus, was also found guilty of tax fraud when at Real Madrid.
He was accused of having avoided paying millions in taxes due on his image rights between 2011 and 2014. He too avoided jail but was ordered by a Spanish court last month to pay more than €3.5 million, part of a broader 18.8-million-euro payout agreed between his lawyers and Spain's taxman.
Ronaldo received a two-year jail sentence immediately commuted to a fine of €365,000 and another penalty of 3.2 million euros, according to the sentence.
Barcelona's Lionel Messi, once Ronaldo's big La Liga rival, paid a two-million-euro fine in 2016 in his own tax wrangle and received a 21-month jail term.
The prison sentence was later commuted to a further fine of €252,000, equivalent to €400 per day of the original term.
Messi and his father Jorge Horacio Messi were found guilty of using companies in Belize, the United Kingdom, Switzerland and Uruguay to avoid paying taxes on 4.16 million euros of Messi's income earned from his image rights.
Barcelona defender Javier Mascherano also agreed a one-year suspended sentence with authorities for tax fraud in 2016.