Casemiro's first-half header had Madrid 1-0 up and in total control against Eusebio Sacristan's strugglers at Santiago Bernabeu on Sunday.
But, within 10 second-half minutes, Cristhian Stuani's penalty and Portu's header had earned Girona's first win away to Madrid and moved them four points clear of the relegation zone.
Sergio Ramos was sent-off in the last minute as he tried to equalise, the Madrid captain catching a defender with a high boot when desperately attempting an overhead kick.
Solari, though, claims he will not prioritise cup competitions over the league despite Madrid's deficit to last season's table-toppers Barcelona and a busy fixture list.
"There's always the league," he said. "We have to get up quickly and keep going, all three competitions are still open for us.
"We came from a very hard journey, we paid for that effort. We tried to overcome, to be fresher with the changes, but we did not achieve it."
Luka Modric's absence due to suspension appeared to leave Madrid weak in the centre of midfield with Douglas Luiz beating Casemiro too easily in the build-up to Girona's winner.
"It is always a cliche to think about the one who is not in [the team]," Solari added.
"We have to face what we are in. This is a squad with great players, it did not come out and that's it."
Marcelo, who has been regularly left out in favour of Sergio Reguilon by Solari, had a difficult day, but the Madrid coach would not single out the defender for criticism.
"Football is a collective sport and the field is covered with all the players," he said when asked if Madrid's defensive problems stemmed from their left.
"Girona came out very well, very strong and they grew in the second half. We did not find the depth when we were dominated."
Madrid are next in action on February 24 when they travel to take on Levante.