In the main comic storylines, Batman did not kill Superman. Their relationship is complex and filled with challenges, but not fatal confrontations. Usually, they find ways to work together or resolve their differences without resorting to killing.
Superman has incredible physical abilities that give him a huge advantage at first glance. But Batman is known for his preparation and ability to find solutions to seemingly impossible problems. Naruto's ninjutsu skills are also not to be underestimated. If the fight takes place in a setting where Naruto can manipulate the environment using his earth - style jutsu, he can create obstacles for Superman. Batman could then use his gadgets to further disable Superman. So, it's not clear - cut. If they all fight fair, Superman might have the upper hand, but with teamwork and strategy, Naruto and Batman could potentially take him down.
Batman won against Superman because he was able to think several steps ahead. He anticipated Superman's moves and had the right tools and tactics ready. Plus, he knew how to play on Superman's moral code and emotions to throw him off balance.
It varies depending on the comic series. Sometimes it's through a mutual enemy's plot that brings them face to face and makes them realize they need to team up.