Ferrer had won in straight sets in his four matches leading up to the finals but found himself down a set early after the world No. 11 Almagro scored four first-set aces to take the set 6-4.
The world No. 5 Ferrer responded well in the second and third sets, using five aces to win the title in just under two hours of work on the red clay at Buenos Aires Lawn Tennis Club.
Ferrer won 79 percent of points on first serve and 3-of-11 break points in his second finals appearance of 2012.
The Spaniard Ferrer is now 13-1 this year and improved to 9-0 against Almagro for his career.
Ferrer took home $82,900 for his finals victory while Almagro banked $43,665 for his second-place finish.