Souza scored the winner for the Brazilians with a 31st minute free kick but his effort was overshadowed by the incident involving team mate Jonas late in the game.
In the 79th minute, Jonas had a shot saved by Edigson Velasquez and hit the post from the rebound. He then collected the ball, rounded the keeper and somehow shot wide with the goal at his mercy.
The hosts had Juan Mahecha sent off in the 69th minute for a second bookable offence, one of six red cards in four games played on Wednesday.
The match, played at 2,700 metres above sea level in the colonial city of Tunja, was preceded by an angry exchange between directors of the two clubs.
The argument broke out after a Gremio director said he was worried that the 140-kilometre journey by road from Bogota to Tunjamight not be safe for his team, which angered the Colombian club and local authorities.
The spat was eventually patched up.
Gremio have four points from two games in Group Seven, behind leaders Universidad de Chile on goal difference.
Javier Villafraz scored from a 67th minute free kick to give Venezuelan champions Deportivo Tachira a 1-0 win over Ecuador's Deportivo Cuenca in Group Two.
Tachira had Julio Machado sent off in the 38th minute for insulting the referee after having a goal disallowed for handball and Cuenca's Jose Guerron was dismissed for a second bookable offence in the 62nd minute.
Tachira went level with leaders Boca Juniors on six points.
Guadalajara went top of Group Six by beating Caracas FC 1-0 with an 80th minute header from defender Aaron Galindo, despite having Jonny Magallon sent off in the 58th minute.
The Mexicans have seven points from four games, one more than their Venezuela opponents.
Chilean side Everton, who have four points, and Argentina's Lanus, who have two, stayed third and fourth respectively after drawing 1-1 in Vina del Mar.
Diego Gonzalez scrambled the ball in for Lanus in first-half injury time and Ezequiel Miralles levelled from a controversial penalty in the 55th minute.
Oscar Cornejo (Everton) and Rodolfo Graieb (Lanus) were sent off after clashing in the 57th minute.
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