The Three Lions cruised into the final four of this summer's Euros on Saturday night thanks to a 4-0 victory over Andriy Shevchenko's side at the Stadio Olimpico in Rome.
England had four players threatened - with three of those starting - by the possibility of suspension for the semi-finals of the competition if they had picked up a yellow card.
Phillips was among those walking a tightrope in Italy but the Whites midfielder alongside Harry Maguire, Declan Rice and Phil Foden came through unscathed and will be available to face Denmark at Wembley on Wednesday.
Southgate was afforded the chance to remove Phillips from the game - who had played every single minute of the tournament prior to his substitution - with the Three Lions in complete control.
The central midfield pairing of the Thorp Arch academy product and West Ham's Rice were both substituted around the hour mark as Southgate had the final four clash in mind.
"We were able to get the players off who were on a yellow card," the England boss reflected post-match.
"There's also a couple who had knocks but we've known we had players we needed to look after physically.
"We know across seven games the squad is so important, trying to give people a breather at the right time. We learned a lot from Russia in that instance.
"We were trying to balance players with knocks and yellow cards. 'Do we take the centre-back off? Because we've the game sewn up he won't need to make a tackle."
Southgate used all five substitutions after the interval in a bid to freshen up his side and hand a rest to those who needed it.
"It's a strange feeling," he continued.
"I'm thinking of the lads we didn't get on the pitch - Conor Coady, Ben Chilwell, Sam Johnstone, Aaron Ramsdale, they're the ones making this team successful. The spirit in the group is phenomenal.
"Whoever comes in does the job, whoever isn't in - it is really difficult to leave three out of the matchday squad - the squad mentality is fantastic. That's uppermost in my mind, looking after those guys.
"I'm spending more energy worrying about the three I have to leave out because they're all good players. None of them deserve to be left out. They're all giving everything in training.
"None of it is because I don't think they're up to the level but we have to make the decisions. We have to make the right call for the right game with the right system. All of the players have been brilliant, tonight all the way through the group they've been fantastic."
On the victory itself, he added: "It's fabulous. I suppose it's still sinking in that it's another semi-final - three in three years.
"We want to go two steps further. I know what will be happening at home. It's lovely to see everyone on a Saturday night, beer in hand. They should enjoy it. It's been a long year for everyone. I'm chuffed that these two performances have brought so much happiness to people.
"It's fabulous for our country - a semi-final at Wembley. Everyone can really look forward to that - it's brilliant."