During the next years, Panathinaikos were again champions in 1961, 1962, 1964, 1965, 1969 and 1970. Moreover, the team won two more Greek Cups, in 1967 and 1969. Also, during these years, a long process of rejuvenation took place in the club. Notable players retired, such as Panakis, Linoxilakis, Takis Loukanidis and Andreas Papaemmanouil, and the team had to count on young players like Domazos, Antonis Antoniadis, Anthimos Kapsis, Kostas Eleftherakis and Takis Ikonomopoulos.Stjepan Bobek was the main contributor to this process. In 1963, he became the clubs head coach, changing the playing style of the team to a 4–3–3 and created a new team based on young players (the Bobeks rejuvenation). Under his guidance, Panathinaikos won the Championship of 1964 without a loss, making them one of the two teams that has won the Greek Championship (with its modern system) undefeated Notable players of the team included Panakis, Domazos, Takis Ikonomopoulos, Totis Filakouris, Frangiskos Sourpis and Aristidis Kamaras.With the establishment of the Greek military regime, the president of the club, Loukas Panourgias, was forced out of the presidency. The contract of Bobek was canceled by the State, while Apostolos Nikolaidis, the old player, manager and official of the club, went on trial. In 1967, the great Béla Guttmann came as coach, but he soon left and ex-player Lakis Petropoulos was appointed. Under his guidance, Panathinaikos won the championships of 1969 (with a double) and 1970.Puskás years and the epic road to Wembley

1970–71 European Cup finalists

In 1971, under the guidance of Ferenc Puskás, Panathinaikos were 1970–71 European Cup finalists, the first and only Greek team until today, losing 2–0 to Ajax at Wembley Stadium.



In the road to the final, they eliminated Jeunesse Esch, Slovan Bratislava, Everton and Red Star Belgrade. Notable players included the captain Mimis Domazos, Anthimos Kapsis, Aristidis Kamaras, Kostas Eleftherakis, Totis Filakouris and the goalkeepers Takis Ikonomopoulos and Vasilis Konstantinou. Antonis Antoniadis was the top scorer in the competition scoring ten goals.




In the same year, Panathinaikos played for the 1971 Intercontinental Cup (due to the refusal of Ajax to participate), where they lost to Uruguayan club Nacional (1–1 in Greece, 2–1 in Uruguay)



Totis Filakouris was the scorer for the Greek club.



During the last amateur years of Greek football, the Trifolium won one more Championship in 1972. Antonis Antoniadis was again top scorer with 39 goals (also second in Europe). His record remains until today in the Greek league.With the collapse of the military regime, Apostolos Nikolaidis became again active for the club and was appointed honorary president of Panathinaikos. In 1975, one of the greatest coaches of his era, the Brazilian Aymoré Moreira, who mainly worked in Brazil (World Cup Champion with the Brazilian national team in 1962), was appointed. After a year-and-a-half of poor results, however, he was replaced by Kazimierz Górski. With Górski, Panathinaikos won the double in 1977, followed by a Balkans Cup victory in the same year. Notable foreign players who played for the team during the late 1970s include Juan Ramón Verón, Araquem de Melo and Óscar Álvarez.