However, with the Poland and Celtic number one fit and ready again, the Parkhead boss swapped the two keepers around for the visit of the Dons.
A Georgios Samaras double which followed Scott McDonald's first-half opener leapfrogged Celtic back over Rangers at the top of the SPL table by two points, with the Gers holding a game in hand.
"They took the news in a very professional way," Mowbray said.
"You make decisions every week, Zheng Zhi or Barry Robson, Fortune or Samaras, Lukasz or Artur.
"Those are the decisions you make every single week in every position so it was no harder than any other conversation you have with a footballer.
"I think they have great respect for each other, they are the same nationality and work very closely in training.
"Lukasz was very supportive of Artur and focused on making sure he was ready for the game."
There were times, though, when the home side could have played without either keeper, such was the one-side nature of the game.
Mowbray, though, tried hard not to get too excited about a comprehensive scoreline which could have been doubled at least had it not been for the woodwork and Pittodrie keeper Jamie Langfield.
"You are never totally satisfied as a coach," the former Hibernian and West Brom boss said.
"Wednesday night against Hapoel was a good performance, the game over in Hamburg was a good performance and away to Moscow was a good performance.
"There has been periods in the season where we have been very good, but that has been punctured by the odd game where we have dropped points.
"The key is to believe what you are doing and make sure that the players continue to believe that is the way to win football games."
One player believing is defender Andreas Hinkel, who was pleased with the patience the home side showed in the first half as they battled against a packed Aberdeen defence before getting the breakthrough through McDonald.
He said: "We have three wins in a row now but it is difficult when the opponents play deep.
"Sometimes it takes time to score and you have to keep the ball and wait.
"The first goal was a good example of that, they slept and we took advantage.
"Sometimes it is difficult but I hope we can keep this style, keep the ball and wait for the chance and then the second half becomes totally different from the first."
Mark McGhee raged at "stupid" defender Jerel Ifil for receiving a red card for appearing to lash out at Samaras after they clashed near the touchline, leaving the visitors with 10 men for the last 35 minutes.
But the Dons boss was more light-hearted when discussing the injury-time substitution of youngster Fraser Fyvie, who had himself came on for Derek Young just after the break.
McGhee said: "Fraser is all right, he hurt his groin. He's a wee boy, he's only 16. He is another one who has a bit immaturity about him and feels pain a bit worse than he should - but he will get there."