Les Bleus fell behind to an early penalty from Robbie Brady but hit back thanks to a second-half double from Antoine Griezmann to book their spot in the last eight.
Deschamps took off N'Golo Kante for Kingsley Coman and changed from a 4-3-3 formation to a 4-2-3-1 system in the second half - a switch that fuelled France's fightback.
The ex-Marseille boss has come under scrutiny for a perceived lack of clarity over his preferred starting XI, having juggled with a few different setups at the tournament so far.
However, Deschamps has hit back by rejecting the suggestion his use of Blaise Matuidi against Republic of Ireland was a "failed gamble".
"I don't gamble with my system," he told a news conference.
"I take these decisions based on discussions with my players but when things don't work out it's my fault. I take responsibility for that. Maybe we shouldn't have started this way, who knows?
"My substitutes can always contribute, not just tactically. It's about willpower and determination. We needed to shake things up. In the second half we saw more fluidity."
A quarter-final clash against England or Iceland awaits at Stade de France next Sunday, when, according to Deschamps, there will be no guarantee man of the match Antoine Griezmann will keep his place in the starting lineup.
"I know that Antoine normally plays up front but he's been good for us out wide as well," Deschamps continued.
"He showed his skill and [effectiveness] in front of goal. You need to find a good balance and we were balanced in the second half.
"That was the choice I made today and I might do it again. As I did against Romania with Anthony Martial playing and with Dimitri [Payet] in the middle. I've got some time to think about it."
Deschamps insisted the options presented by his versatile squad is an advantage as he looks to ensure France are difficult to plan against.
"I've got 23 players here, they're all available," he said.
"Just look at the German team, they've changed things around a lot.
"The only team who didn't change things around were Croatia. People said they were going to make the final. It doesn't always go as you think it will go.
"Our opponents only have to look on the TV to see [how] we're going to play, they will know. It's important to have different solutions."