Seidler, who founded private equity firm Seidler Equity Partners, purchased the team along with his uncle Peter and businessman Ron Fowler in 2012.
He took over as chairman after becoming the club's largest stakeholder in 2020 and last season its payroll was the third highest in Major League Baseball.
"The Padres organisation mourns the passing of our beloved Chairman and owner, Peter Seidler," Padres CEO Erik Greupner said in a statement.
"Today, our love and prayers encircle Peter's family as they grieve the loss of an extraordinary husband, father, son, brother, uncle, and friend.
"Peter was a kind and generous man who was devoted to his wife, children, and extended family. He also consistently exhibited heartfelt compassion for others, especially those less fortunate. His impact on the city of San Diego and the baseball world will be felt for generations.
"His generous spirit is now firmly embedded in the fabric of the Padres. Although he was our Chairman and owner, Peter was at his core a Padres fan. He will be dearly missed."
No cause of death was given. Seidler had battled lymphoma in the past and underwent a medical procedure in September that prevented him from attending games for the rest of the season.
Seidler and wife Sheel have three children.
The Padres invited fans to gather outside of Petco Park on Tuesday to pay their respects.
