Matthew Amoah made it 3-1 to Milovan Rajevac's side but the momentum swung back to Japan after goals from Keiji Tamada and Shinji Okazaki leveled the scores before Inamoto's winner.
Yoshito Okubo was guilty of a bad miss early on before Tamada showed his strike partner the way, sliding in to fire home a right-wing cross from Makoto Hasebe in the 21st minute.
Villar saved a low strike from Honda that appeared to be going wide and there was one moment when there appeared to be space inside the Paraguay box but any prospects of Japan capitalising were undermined by an awful cross from substitute Keiji Tamada.