Midfielder Endo, winning his 149th cap, was allowed far too much space to stroll forward before hitting the low, eighth minute shot across Palestine goalkeeper and skipper Ramzi Saleh into the corner of the net.
The 34-year-old shrewdly kept his shot low under the stiff breeze that Japan were playing into at the Newcastle Stadium but Saleh seemed to dive too early and should have kept it out.
The chance was one of several Japan created as Javier Aguirre's side predictably dominated the West Asians, ranked 115th in the world by FIFA and competing in the tournament for the first time. They added a second in the 25th minute when striker Shinji Okazaki used his head smartly to stoop low and redirect a wayward volley from Shinji Kagawa past Saleh from close range.
The Blue Samurai, a record four-times winners of the tournament, dominated possession and pinned the Palestinians back for the majority of the 45 minutes with goalkeeper Eiji Kawashima a passenger for most of the half.
The Palestinians gifted their opponents the chance to add a third four minutes before the break when defender Musab Battat clumsily bundled over Kagawa in the penalty area. Keisuke Honda, player of the tournament four years ago, stepped up to send Saleh the wrong way with the spot kick.
Iraq will play Jordan in the other Group D clash in Brisbane later on Monday.