The 21-year-old, who starred at the recent Confederations Cup, finally joined Barcelona in May following much speculation about a move to the Camp Nou.
However, Rummenigge says that despite Guardiola's eagerness to sign Neymar, Bayern persuaded him that capturing Mario Gotze from Borussia Dortmund was the right option.
"We had a clear vision of what kind of player we wanted to buy," Rummenigge told Sport Bild. "We discussed that matter with Pep [at a meeting in Zurich].
"Really, there were only two players of that quality of whom we knew signing them was possible - Neymar and Mario Gotze.
"We then told Guardiola about our experiences with players coming directly from South America."
Gotze cost Bayern £32m after they triggered a release clause in his contract.