"We were surprised to learn he wasn't," former Yankees player and executive Bob Watson said.
Watson and a 16-member Hall panel changed that Monday, electing Ruppert, longtime umpire Hank O'Day and barehanded catcher Deacon White for their excellence through the first half of the 20th century.
The trio was picked from by the Hall's pre-integration panel — part of what once was known as the Veterans Committee — and gave the shrine exactly 300 members.
"The family is so thrilled," great-grand-nephew K. Jacob Ruppert told The Associated Press by phone. "His mark is now indelible."
"Growing up, I was under the impression that he was inducted sometime in the 1940s or 1950s. But I guess it never happened. Some things in history aren't appreciated. If it's not in the here and now, it's off the radar screen."
The Hall announcement was made at baseball's winter meetings. Induction ceremonies will be held July 28 in Cooperstown, N.Y., and the younger Ruppert is planning his first visit to the shrine.
"I'll grab some of my cousins, too," he said.
Ruppert and a partner bought the Yankees in 1915 and quickly turned them into a force. Under Ruppert's reign, the Yankees bought Ruth from the Boston Red Sox and presided over the club's first six World Series championships.
"This was the Colonel's toy. He liked to bring big stars to the team and built them a place to play, much the same way George Steinbrenner did," Ruppert's relative said.
O'Day umpired in 10 World Series, including the first one in 1903. He worked 35 years and made one of the most famous calls in the game's history, ruling Fred Merkle out in a 1908 play that long lived in baseball lore as "Merkle's Boner." He was the 10th umpire to go into the Hall.
White played from 1871-1890, starting out as a catcher without a glove and later moving to third base. He was a three-time RBIs leader, once topping the league with 49 RBIs when baseball hardly resembled the game it is today.
The new members will be honoured along with anyone chosen in January in voting by the Baseball Writers' Association of America.
Hall of Famer and panel member Phil Niekro credited two historians on the panel, Peter Morris and Tom Simon, with helping to illuminate the accomplishments of those who are long gone.
"It's tough to go back into the 1800s and bring that to life," Niekro said. "It was so different then — five strikes, eight balls, batters can tell the pitcher where they want it. Can you imagine? I couldn't have done that if I tried, not with my knuckleball."
Ruppert, O'Day and White all died in the 1930s — the first Hall class was selected in 1936.
Hall of Famers Bert Blyleven, Don Sutton, Pat Gillick and Niekro were among the voters who considered 10 candidates. Former NL MVPs Marty Marion and Bucky Walters also were on the ballot.
It took 75 per cent (12 votes) for election. Ruppert and O'Day each got 15 votes and White drew 12. Bill Dahlen got 10 and Marion, Walters, Sam Breadon, Wes Ferrell, Tony Mullane and Alfred Reach each got three votes or less.