Southgate, who is expected to recall the attacker for Tuesday's last-16 tie with Colombia, added that the physical condition of his players is his priority going into next week's clash.
"[Kane] totally understood, 100% team-first," the manager told Sky Sports News.
"He said 'look, I know everyone says I want the Golden Boot - of course it's something I want to do - but the main thing is getting the team through the first knockout'. He was excellent on that, showed real leadership and understanding of the big picture.
"The most important thing for me is the players are in the best physical condition for the game. I don't think mentally we lose anything, because they know we've made changes and they know Belgium weren't their full team as well."