England's final home game of the 2023 ended with a 2-0 win over the fourth-worst side in Europe, sealed by an early own goal by Enrico Pepe and Harry Kane's 75th-minute strike.
It was a measure of England's display that they did not muster a shot on target until the 64th minute when Trent Alexander-Arnold drew an easy save from the Maltese goalkeeper.
England had already qualified for next summer's European Championship in Germany and Southgate says he is not worried about his team sleepwalking into the finals.
"No, it's not a worry because sometimes when players have so many matches they almost self-regulate," the England manager said.
"You know there's a certain level you need to hit to beat Italy here and you know you don't have to hit that level to win today's game.
"And although you'd think everybody would be at the same level all the time, that's not the reality of football.
"There are nights where subconsciously you just do enough to win and that's a little bit where we were tonight.
"We wouldn't be able to play [like that against] the teams we've got in March [Brazil and Belgium in friendlies], we wouldn't get away with it. The players would have a different level of motivation.
"This week was always going to be difficult. We've already qualified, the players are in the middle of a load of matches. We're trying to look after a few physically.
"We were flat, I accept that. That's where we were but I'm not going to get into the players about that. I know why.
"They've won another game of football and it could have been by more."
The result might have been more comfortable but Kane was denied a first half penalty after appearing to be caught by Malta goalkeeper Henry Bonello and was instead booked for diving.
"I thought the yellow as a bit harsh, I thought there was definitely contact from the goalkeeper, I thought that was pretty clear," said Southgate, who added that he was "not sure" why Declan Rice's strike to make it 3-0 was ruled out for a Kane offside by the VAR.
Southgate picked out Alexander-Arnold, Phil Foden, Marc Guehi and debutant Cole Palmer as positives, and said he wanted his side to end the year on a high in Monday's visit to North Macedonia.