European and Spanish champions Barca dominated the match at the Coliseum but could not beat keeper Miguel Angel Moya and Juan Valera stunned the visitors with a goal in the 67th minute.
The defender headed in from a corner and then the rest of his team manned the barricades for a desperate siege in the closing minutes.
Earlier, Cristiano Ronaldo scored two penalties as Jose Mourinho's Real Madrid side came back from a goal down at the Bernabeu to beat their long-suffering neighbours who had goalkeeper Thibaut Courtois sent off in the 22nd minute.
Real's 13th consecutive win in all competitions put them on 34 points from 13 games and moved them six ahead of Barca, who have to visit the Bernabeu in two weeks' time.
"It's a shame because we are further behind, but we gave our all today," Spain and Barca striker David Villa told reporters.
"Getafe kept it very tight and their keeper was very good."
Lionel Messi led Barca's charge at the other end and was unlucky to have a goal ruled out for offside in the 90th minute.
Belgian Courtois, on loan from Chelsea, brought down Karim Benzema in a one-on-one the area and was sent off in the 22nd minute. Ronaldo netted from the spot and Atletico's chances of an upset slowly evaporated.
"It's clear we have had similar situations in the area as those today which didn't up with the same result," Atletico coach Gregorio Manzano said of the Courtois red card.
"It may have been a penalty but it wasn't a sending off. In an important game like this it can be decisive."
