Seven players were given their first starts of the tournament, with Southgate keen to keep his core players fit for the knockout rounds.
Defeat to Belgium ended England's 12-match unbeaten run, though, and there are fears that the momentum that has been steadily building may have been halted.
"Whatever happens next week [in the knockout rounds], that was the right decision as far as I'm concerned," he said. "People will say that will only be the right decision if we win but it was the right decision because we could potentially be going into another match that could go into extra time and risking players we didn't need to risk.
"This was a game we wanted to win but the knockout is the biggest game for a decade for us, and we had to make sure our key players were preserved. You have to look at the bigger picture sometimes and make decisions which, in some quarters, might be criticised. But everyone understands - in the dressing room and in the group - what we're trying to do.
"We don't like losing and don't want to lose matches, but the primary objective from the evening we've got. And if we'd put Harry on for 10 minutes and someone had raked his ankle, that would have been ridiculous. The knockout game is the important one. Of course we have a responsibility to the supporters, and the support in the stadium was absolutely outstanding tonight. The support and encouragement from home has been brilliant.
"But when you're a leader and a manager, you have to make decisions which are right for your group to achieve the primary objective. Sometimes those decisions will be criticised. I understand that. But only one person makes that decision with all the full facts and managing a tournament in mind: physically, medically, tactically for the benefit of the group. I'm entirely comfortable with the decision. Sometimes you have to make decisions for the bigger picture."
England now know that they will face Colombia in the first knockout round next Tuesday, while Switzerland or Sweden potentially await in the last eight.