The victory at the Calderon means Atletico have won 10 La Liga home games on the trot for the first time in almost 40 years.
They stretched their advantage over third-placed city rivals Real Madrid to seven points after the stuttering champions were held to a 0-0 draw at bottom side Osasuna on Saturday and had Kaka sent off.
Midfielder Thiago nodded a dominant Atletico ahead in the 31st minute and Falcao doubled the home side's lead from the penalty spot seven minutes later after Arda Turan was felled by Zaragoza defender Cristian Sapunaru.
It was the seventh successful penalty conversion this season by the Colombia striker, who is coveted by several of Europe's wealthiest clubs, and took his league tally for the campaign to 18, nine behind Barca forward Lionel Messi and two ahead of Real's Cristiano Ronaldo.
Real Zaragoza have a record of seven wins, 11 losses and one draws which puts them in 13th place, only five points above the relegation zone.
Atletico had nine shots, including five on target.
Falcao took four shots.
The combination of Filipe Luis to Arda Turan was the most common during the match as the two players connected 17 times.
Los Blanquillos's attackers only managed four shots and only one on target.