The League Two club confirmed on its official website that it has agreed to sell a share to Sports Alpha Capital, the group that has named the former Brazil international as one of its investors. Northampton did not say how big the stake will be.
Chairman Kelvin Thomas said: "Deals involving football clubs always involve many moving parts and often take a little longer than hoped, but we are very pleased that the process is now moving forward.
"We all saw the enthusiasm and passion that both the supporters and Sports Alpha showed when Pato and others from the group were present at the match against Newport, and we believe that enthusiasm will only grow."
BBC Sport reported in August that a consortium including Pato was set to take a majority stake, although it understood the Brazilian was involved without fronting the group.
The consortium had held talks about buying Colchester United earlier this year before walking away. The Independent Football Regulator and the English Football League approved the investment on Friday 4 September, according to Brazilian reports, which also name London-based investment manager Gemcorp Capital as part of the group.
Northampton, who dropped into the fourth tier last season and have spent only one campaign in the top flight, in 1965-66, are a long way from the stage on which Pato made his name. The forward, who turned 37 this month, scored 63 goals and provided 18 assists in 150 appearances for AC Milan and won the Serie A title with them in 2010-11.
His time in England was brief. Pato joined Chelsea on loan from Corinthians for the second half of the 2015-16 season and scored on his debut, from the penalty spot, in a 4-0 win at Aston Villa.
He retired at the start of 2025, with São Paulo his last club. Now he is set to return to English football in a very different role, as part of the ownership of a club in League Two.