The Belgian attempted to keep out a deep cross from Juan Fuentes but the ball bounced off his arm and into the net after 54 minutes.
Los Rojiblancos were outfought by the Catalans, who limited the visitors to very few goalscoring opportunities due to their discipline and hard work.
The result meant Diego Simeone's side missed the opportunity to go top of the Primera Division table after Barcelona could only draw at Osasuna. Instead they slipped one point behind Gerardo Martino's men, while allowing allowing Real Madrid to reduce their deficit with their neighbours to just two points.
Aguirre's side, meanwhile, moved up to fifth in the table and are proving to be a force to be reckoned with at home.
The two teams came into the game in contrasting form, though. Simeone's side had won all eight of their opening games, while the hosts had lost three games on the trot.
Espanyol striker Sergio Garcia had been a doubt in the build up to the game after missing training during the week, but was included in Javier Aguirre's starting line-up.
David Villa, who missed Spain's final World Cup qualifiers with an ankle injury, returned for the visitors, as did Raul Garcia, meaning Arda Turan started on the bench, while centre-half Toby Alderweireld made his debut for Los Rojiblancos, with Joao Miranda injured.
The first half was a cagey affair, with both teams denying each other space, which made for few periods of prolonged possession.
Neither side managed a shot on target in the opening 45 minutes, although Atletico midfielder Koke struck the outside of a post from six yards out after a side pass from Diego Costa.
The Brazilian then barged his way through the Espanyol defence just before the break, but when he came to shoot, pulled his effort well wide of the near post.
Courtois was called into action for the first time in the game early in the second half, diving low to his right to keep out a shot from Manuel Lanzarote, and then catching a weaker effort from the midfielder seconds later.
However, a few minutes later the Belgian was picking the ball out of his own net.
Fuentes sent in a troubling cross from the left-hand side towards Sergio Garcia, but the striker did not touch the ball and it bounced off Courtois' arm and trickled into the bottom corner.
With Atleti needing to turn the game around, Arda was brought on for Raul Garcia, while fellow attackers Adrian Lopez and Cristian Rodriguez also coming on. Their introduction had little impact.
Diego Costa did manage to put the ball in the net from a free-kick by Koke, but was several yards offside.
The striker was then inches away from finding a legitimate equaliser, played in by Villa but unable to steer his shot inside the far post from a tight angle.
Atleti's desperation for an equaliser saw Courtois come up to contest a corner, but when Espanyol broke, the goalkeeper had to commit a foul to stem the counter, earning himself a yellow card to round off an unfortunate evening for the talented 21-year-old.