Verstappen and Ricciardo were second and third behind Lewis Hamilton in qualifying, but they are carrying 20 and 25-place penalties this weekend, having both taken new power units at Monza, with Ricciardo also running a new gearbox.
While Red Bull was disappointed to have to give up those grid positions, the engine changes were part of a plan aimed at maximising the team's chances at upcoming races that should suit its RB13 more.
“It's frustrating not only for the penalties, but we have nearly no downforce on,” Marko told Autosport.
“And that in the rain is why we lost out so much. So not to make a mistake, and be second and third under these conditions, shows what potential is in the car.
“But we don't regret anything. It's not just about (the next race in) Singapore, it's Malaysia, and Suzuka, they're all circuits for us.”
Horner said Red Bull could take pride in its performance in tough conditions.
“It's a shame that we have to take the penalties, but we're enjoying the qualifying for now,” he said.
“Second and third is a fantastic performance from both of the drivers.
“Even with the penalties from where we start on a mixed up grid, there are still opportunities at a track where you can overtake.
“We got all the timings right today. The pit wall did a great job, and we picked the right tyres for the right conditions.
“Both of the drivers today have done a phenomenal job.
“It is slightly academic for tomorrow as the penalties see both drivers starting down the grid but we will be hopeful of making good progress as the race unfolds.
“At the very least the fans deserve to see an exciting Italian Grand Prix as a reward for their support and waiting in the rain for the late show today.”