Anderlecht acquired Pareja in 2006 for €2 million as a replacement for Vincent Kompany, and the former went on to be a teammate of compatriots Lucas Biglia, Nicolás Frutos and Cristian Leiva.

He made his La Liga debut on 14 September, playing the full 90 minutes in a 1–0 away victory over Recreativo de Huelva,[15] and scored his first goal in the competition the following 11 January to help salvage a point at home to UD Almería (2–2).

[19] He made his Russian Premier League debut late in that month, featuring four minutes in a 4–2 home win against FC Tom Tomsk.

[20] After missing out several matches throughout June and July 2011 due to international commitment, both Pareja and compatriot Marcos Rojo were fined for returning late to the club.

[22] Pareja was handed a three-match ban after being sent off for a hard tackle on PFC CSKA Moscow's Vágner Love in November 2010,[23][24] being suspended even harsher (four) in October of the next year following a match against FC Zenit Saint Petersburg.

[26] After featuring regularly in his second season, Pareja appeared only 12 times in his third, due to rotations with Salvatore Bocchetti and Juan Insaurralde[27][28] as well as physical problems.

[33] On 3 January of the following year, whilst celebrating his 100th appearance in Spain's top flight, he scored the game's only goal at home against RC Celta de Vigo, through a direct free kick;[34] on 23 April, early into a Europa League quarter-final tie at Zenit, he suffered an anterior cruciate ligament to his right knee, going on to be sidelined until the end of the year.

[36] Having acted as team captain for the first time on the 28th, in a 0–0 away draw to Villarreal CF,[37] he was named by manager Jorge Sampaoli as one of the four skippers early into the new season.