Neymar scored six goals during Santos run to the 2011 Copa Libertadores Finals, tying him for third top goalscorer,^[34]including the clinching goal of Santos' 4–3 aggregate win over Cerro Porteño in the semifinals.^[35] In the two-legged final, Santos faced Uruguayan side Peñarol and drew the first leg 0–0 in Montevideo.^[36] At home in the second leg, Neymar opened the scoring in the 46th minute as Santos held on for a 2–1 win and Neymar won Man of the Match honours.^[37][38]The win brought Santos their first Copa Libertadores triumph since 1963, when Brazilian legend Pelé was playing for the club.^[39][40]

In September 2011, Santos president Luis Ribeiro threatened to report Real Madrid to FIFA following reports that they had attempted to sign Neymar to a pre-contract agreement and denied that such an agreement was in place.^[41] On 9 November 2011, Neymar and Santos agreed to a contract extension that would see the player stay with the club until after the 2014 World Cup in Brazil. The deal reportedly increased Neymar's wages by 50%, to the levels that top European clubs would be paying him.^[42] On 14 December 2011, Neymar scored the opening goal for Santos as they defeated Kashiwa Reysol 3–1 in the semi-finals of the FIFA Club World Cup at the Toyota Stadium in Toyota, Japan, but failed to score against Barcelona in the final on 18 December 2011, where Santos were defeated 4–0, finishing as runners up in the competition.^[43] He won the 2011 FIFA Puskás Award for scoring a sensational solo goal in the Brasileirão Série A against Flamengo, in a 5–4 loss. On 31 December 2011, he won the 2011 South American Footballer of the Year award for the first time, by a record margin, following in the footsteps of Diego Maradona, Romário, Pelé and Zico.^[44]

2012 season

On 5 February 2012, when he turned 20, he scored his 100th goal as a professional football player, against Palmeiras in the Campeonato Paulista.^[45][46] On 25 February 2012, Neymar scored two goals, one of whom from 25-yards and assisted with two, to help his side to a 6–1 win over Ponte Preta.^[47] On 7 March 2012, Neymar netted a hat-trick as Santos saw off Brazilian rivals Internacional 3–1 in the Copa Libertadores Group stage match.^[48] On 29 March, he scored a brace against Guaratinguetá in a 5–0 victory.^[49] In the fixture against São Paulo on 29 April 2012, Neymar scored a hat-trick with the match ending 3–1.^[50] Thereafter, he went on to score twice in the 1st^[51] and 2nd legs^[52] in the 2012 Campeonato Paulista Finals against Guarani, which ended 7–2 on aggregate. Neymar finished the2012 Campeonato Paulista with 20 goals and was voted the Best player and Best Forward, and Santos were crowned champions. He was joint top scorer in the Copa Libertadores with 8 goals, after Santos were beaten over two legs by eventual champions Corinthians in the semi-finals.

On 25 August 2012, he scored a brace in the 2–1 away win at Palmeiras.^[53] On 3 November 2012, in the Brasileiro Série A away fixture at Cruzeiro, Neymar scored a hat-trick and assisted Felipe Anderson's goal, to help his side to a 4–0 win.^[54] Neymar finished off the 2012 season in style, first setting-up Victor Andrade's equaliser, then scoring twice, to give Santos a 3–1 home win over Palmeiras on 1 December 2012.^[55] Neymar was voted the Best player of the 2012 Recopa Sudamericana, Neymar scoring in the second leg to win the title 2–0 on aggregate. He finished the 2012 Campeonato Brasileiro Série A with 14 goals and being voted the Best forward. Neymar finished the 2012 season, being award the Golden Ball, Arthur Friedenreich Award and Armando Nogueira Trophy. He was one of three finalists in the 2012 FIFA Puskás Award and finished runners-up behind Miroslav Stoch. He won the 2012 South American Footballer of the Year, retaining his award and winning it ahead of the likes of Ronaldinho. Reports emerged in 2011 that Santos reached an agreement with Barcelona to sign him at a later stage. However, Neymar rejected this in an interview, saying that he had "no agreement with Barcelona or anyone else".