Diego Simeone’s side lost 1-0 to Real Sociedad after Xabi Prieto's 53rd-minute strike, which was proven by television replays to have come from an offside position.
Atletico’s previous record of 800 minutes came from former coach Abel Resino, who was keeper during the 1990-91 season, but on-loan Chelsea man Courtois would have been happier to miss the mark and win the match.
"It is a record for the whole team, not only for me," 20-year-old Belgium international Courtois said after the match.
"I am pleased because it is always nice to set a record, especially one like this, but it is the work of all the players, not only me.
“I would have preferred to win and not have the record."
His last conceded goal in La Liga came on October 28.
Atletico coach Diego Simeone had only last week signed a contract extension until 2017, having won the Europa League in his first season.
However, an early Liga title challenge has stalled, with Barcelona runaway leaders and Real Madrid moving above their city rivals into second place.
"Although we lacked accuracy, we played with ambition but we were unable to hurt our opponents," Argentine Simeone said.
"We will look to improve where we need to improve as a team. This way, we will get back to experiencing what we have done up until now."