Jose Becker, 57, had been swimming at a dam on his property near the town of Rincao do Inferno and was declared missing around 5 p.m. local time on Wednesday.
The Fire Department of Cacapava do Sul sent a team to assist in the search, and it located the body at 11:59 p.m., authorities told ESPN Brazil. No foul play was suspected.
Internacional, whom both brothers played for, tweeted their condolences, while Liverpool posted a picture of Alisson on Twitter with the caption: "You'll Never Walk Alone."
"It is with great sadness that we received the news of Jose Agostinho Becker's death, the father of our ex-goalkeepers Alisson and Muriel," the club said.
Liverpool later issued a statement asking for Alisson's privacy to be respected.
"Liverpool FC is deeply saddened by the tragic death of Alisson Becker's father, Jose, in Brazil on Wednesday," the statement read.
"The thoughts of everybody at the club are with Alisson and the Becker family at this incredibly sad and difficult time."
Liverpool are next scheduled to play Sheffield United at Bramall Lane on Sunday.
Information from Reuters was used in this report.