The 50 year-old former Valencia and Chile boss saw Takehiro Tomiyasu score the only goal of the game at Sharjah Stadium as Saudi Arabia's hopes of lifting the trophy for a fourth time were ended.
Pizzi's men finished second in Group E to reach the round of 16, but the conservative football that drew criticism in their first few games was on display once again as they were knocked out.
Announcing his decision to leave his role, Pizzi told reporters: "I'm happy and grateful for my players, they did what I asked them to do.
"Of course, we did some mistakes but we will learn from them.
"My job with the national team is done, nobody talked with me about renewing my contract.
"I still don't know anything about my next challenge."
Pizzi leaves behind him a disappointing record as Saudi Arabia coach, after guiding the team to four wins from the 10 competitive matches during his tenure.
Highlights of his time in charge include a 2-1 win over Egypt at the World Cup in Russia, and the back-to-back victories in the Asian Cup group stage that gave his side hope of a run deep into the competition.
Returning his thoughts to the defeat to Japan, Pizzi added: "The players have not let me down throughout the entire Asian Cup.
"We must not forget that we played against one of the best teams in Asia, with most of their players participating in the European leagues.
"We chose the best players who deserved to represent the team. I am satisfied with how they performed during the tournament and what they earnestly sought to apply in the games in terms of technical plans and strategies."