The unstoried club took the title, South America's equivalent of the Europa League, without losing any of their nine games in the competition to become only the fifth team in history to lift the trophy undefeated.
"Not many teams have won the title this way, undefeated," said goalkeeper Luis Unsain. "We were extraordinary in defence, Lanus had no chances at goal and we scored three. I think we really deserved our win."
The searing temperatures of the southern hemisphere's summer meant the game was played at a slower pace than normal but the team coached by former Internazionale, Parma and Chelsea striker Hernan Crespo dominated proceedings from the start.
Braian Romero shot just wide early on before Defensa y Justicia took the lead after 33 minutes when Adonis Frias fired a low shot through a packed defence following a nice back heel from Francisco Pizzini.
Romero got the goal his play deserved 17 minutes into the second half when he seized on a short pass back and finished with a cheeky chip.
His 10th goal made him the competition's top goalscorer.
Lanus, who won the competition in 2013, lost their way soon after, picking up three yellow cards in the final 20 minutes and rarely threatening a comeback.
Washington Camacho scored a third for Defensa y Justicia in the final minute when he finished off a rapid counter-attack.
"It was a fair result," said Lanus veteran striker Jose Sand. "They were worthy winners."
Although both clubs are based just south of Buenos Aires, the final was held behind closed doors in Cordoba, 700km away.
It was the first time the Copa Sudamericana has been contested by two teams from the same country.