The Argentine made the "corrective payment" in August after being accused of filing incomplete documents between 2006 and 2009
The Barcelona star was accused of "hiding" more than €4m earlier this year having failed to file complete tax returns between 2006 and 2009, although both the 26-year-old and Messi Snr. denied all wrongdoing.
A court in Gava has now confirmed the duo have made a "corrective payment" of €5,016,542.27, though they will still be required to attend a legal hearing on September 17.
"We have our lawyers and our wealth managers to take care of that and we trust them and they will sort this out," Messi said of the issue earlier this summer.
"The truth is that I don't have a clue about all this and that is why we have people taking care of it."
Messi earns a combined total of more than €40m per year through wages and sponsorship deals, placing him 10th on the latest Forbes rich list for athletes.
The Argentina international is not the only top-level football professional to become embroiled in tax problems this year. At the end of July, Bayern Munich president Uli Hoeness was formally charged with tax fraud after failing to declare on a Swiss bank account.