1999–2000 Club Atlético Boca Juniors season

Alternate kit worn in Copa Mercosur only

The club' s main goal for Apertura was clinching its three consecutive League title for the first time in its history.[1] The squad was reinforced with few players included forward Alfredo Moreno.[2] The race for the title started early against archrivals River Plate during the whole season. Finally, the club finished on 2nd spot just below of Millonarios thanks to key injured players and a 0–2 defeat against River.[3]

For Clausura Tournament the club was reinforced with several players included forward Marcelo Delgado from Racing.[4] The team played a decent season finishing again on 2nd spot thanks to a judicial sanction suspended the game against Newell's Old Boys and deducting 3 points due to a fireworks throwed to the field. In the replay, Newell's won the match and Boca Juniors finished below of Champions River Plate.

Meanwhile, after six years the club returned to play Copa Libertadores and advanced to Quarterfinals defeating archrivals River Plate included a 3-0 landslide in second leg of the series at La Bombonera. In Semifinals the squad eliminated Mexican team America thanks to a Samuel goal in the final minutes of the second leg of the series. In the Finals of the tournament the squad defeated incumbent Champions Palmeiras after a penalty shoot-out series clinching the title after 22 years.

Note: Flags indicate national team as defined under FIFA eligibility rules. Players may hold more than one non-FIFA nationality.

No. Pos. Nation Player 1 GK  COL Oscar Cordoba 2 DF  COL Jorge Bermúdez 3 DF  ARG Rodolfo Arruabarrena 4 DF  ARG Hugo Ibarra 5 MF  COL Mauricio Serna 6 DF  ARG Walter Samuel 7 FW  ARG Guillermo Barros Schelotto 8 MF  ARG Diego Cagna 9 FW  ARG Martín Palermo 10 MF  ARG Juan Roman Riquelme 11 MF  ARG Fernando Navas 12 GK  ARG Roberto Abbondanzieri 13 MF  ARG Christian Traverso 14 MF  ARG Nicolás Burdisso 16 FW  ARG Marcelo Delgado 17 MF  ARG Gustavo Barros Schelotto

No. Pos. Nation Player 18 MF  ARG José Basualdo 19 DF  ARG César La Paglia 20 FW  ARG Antonio Barijho 21 FW  ARG Christian Giménez 22 MF  ARG Sebastián Battaglia 23 FW  ARG Alfredo Moreno 24 MF  ARG José Antonio Pereda 26 FW  ARG Emanuel Ruiz — DF  ARG Aníbal Matellán — DF  ARG José María Calvo — MF  ARG Omar Pérez — DF  ARG Gustavo Pinto — DF  ARG Julio Marchant — FW  ARG Matías Arce — MF  ARG Facundo Imboden — DF  ARG Elías Bazzi