Deschamps took the bold decision to leave the pair out with Kingsley Coman and Anthony Martial starting instead in a 4-2-3-1 formation.
It resulted in a disjointed first-half performance with Les Bleus improving following the half-time introduction of Pogba and Griezmann's arrival after 68 minutes.
Griezmann glanced home the opening goal with just a minute left and Dimitri Payet gave the scoreline a flattering look with France's second deep into injury-time.
"Leaving out Paul Pogba was a tactical decision when we looked at their starting line-up," explained Deschamps. "With their system we needed two scrappers in the middle of the park. Paul Pogba has different attributes.
"With Antoine Griezmann - I know he's not happy, nor is Paul Pogba - but he is doing well. He [Griezmann] played 60 minutes of the first match and I know he's very good at coming off the bench.
"He played for half an hour tonight and made the difference even though I know he would rather have started the game. Often the players that come off the bench can make the difference. So if someone is not up to their usual level I have the option to go to the bench to make the difference."
Switching to a 4-2-3-1 appeared a failed experiment with Deschamps reverting back to the 4-3-3 he fielded against Romania at half-time.
He said: "I made a decision based on the opposition, they crowded the middle so I wanted to put players that can beat men on the flanks.
"We did that to a certain extent but not enough which meant we were imbalanced when we won the ball back. We weren't all working together. That's why I tweaked things at the break, while asking the wide players to move as wide as possible to open up their defence."
One man who has starred in both games is Payet with the West Ham man rapidly becoming France's main attacking threat.
"He's become more consistent, he's putting more into his performances with West Ham," added Deschamps.
"He's always had ability and he's got a lot of confidence. When he is faced with challenges he is always up for the fight. Maybe it took him a while to show all of that but I will stress what I said the other day, I will put him on ice so he can maintain his performance levels."
Although France deserve credit for finding a way to win the game, Albania will be disappointed their brave display did not result in at least a point.
Deschamps said: "Albania played with a lot of heart and spirit. I'm not saying they didn't try to score, they have the ability to counter and they did that a lot in the first half.
"In the second we had a lot of chances but while it was goalless that was a good result for Albania. They got a lot of numbers in defence, and then it's on us to find the answers. We didn't do that in the first 45 minutes. We finally got going but it came late in the day.
"I retain the fact we have six points and have qualified. Certainly we didn't do everything well but if you have seen a team do everything well over the past few days then show me.
"We were laborious in the first 45 minutes but having put so much into the game we showed we could win it at the end. This is becoming a habit and I'd rather we scored a bit earlier."