Paraguayan defender Victor Ayala put the home side one up in the 24th minute and striker Ismael Blanco, man of the match, increased their lead at the Ciudad de Lanus stadium in the second minute of added time in the first half.
It was the third title won by Lanus, a modest club from the Buenos Aires outskirts, after the now defunct Copa Conmebol in 1996 and the 2007 Apertura championship, their only Argentine league title.
"This title cost us a lot of sacrifice, we are a squad that wanted to win things and we achieved that, it's a great joy for the club," Lanus goalkeeper Agustin Marchesin told reporters.
"I felt I owed the team a goal and mine turned out to (be the one) to secure victory," said Blanco.
Ponte Preta, relegated from the Brazilian first division last month, fell at the last hurdle after shocking holders Sao Paulo by eliminating them in their semi-final.
Ayala began the move that led to the opening goal in midfield and finished it after taking a pass from Blanco inside the box to slot the ball past goalkeeper Roberto.
Blanco scored the second from fellow striker Santiago Silva's header into the middle at a corner.
The Copa Sudamericana is South America's second club competition, equivalent to the Europa League.