Juan Carlos Osorio's men, who have played a game more than everyone else in the top flight, moved clear with two wins in four days.
Edwin Cardona and Sebastian Perez struck in the first half at the Estadio de La Independencia in Tunja against Boyaca Chico.
Jairo Castillo hit back just before the hour-mark for the hosts, but they were unable to find an equaliser.
Cardona opened the scoring on 33 minutes, bringing down a long throw in before turning and firing into the bottom corner.
The lead was doubled by Perez in first-half injury time as his 30-yard strike found the bottom corner.
Castillo pulled one back in the 58th minute when Atletico goalkeeper Luis Martinez spilled a shot and the substitute delicately chipped the shot-stopper.
But that was their only goal as a second straight league loss left them sitting seventh.
Atletico Nacional also claimed a 3-1 win over Uniautonoma on Tuesday are now six points clear of second-placed Once Caldas.
Jefferson Duque, Sherman Cardenas and Jhon Valoy were all on the scoresheet.
Third-placed Santa Fe saw their winless league run extended to three matches after a 0-0 draw at Deportes Tolima.
Deportivo Cali claimed their first league win of the season with Robin Ramirez's 30th-minute goal giving them a 1-0 victory at home to Atletico Huila.
