The midfielder scored from the spot after 73 minutes only for Genki Omae to equalise for Shimizu four minutes later at the National Stadium in Tokyo.
Three minutes after the start of extra-time, Shibasaki struck again to score what would be the winning goal.
“I was fouled for the penalty, so it was mine to take,” the 20 year-old said. “The veterans in this team have won so many titles for this club, so to help the club win another one makes me very proud.”
It may be Kashima’s 16th trophy but it is the first for coach Jorginho.
“It’s a big privilege for me to win this title,” said Jorginho. “Not everyone in the world gets an opportunity like this, but the season isn’t finished yet. The most important thing — more important than me — is the players’ desire to keep on working and winning. Getting this trophy today should help me keep the players motivated.”
S-Pulse boss Afshin Ghotbi was left to reflect on what could have been and is confident that his young team have plenty of time to win trophies.
“Overall I was disappointed with our performance in overtime,” said Afshin Ghotbi. “We let in a very bad goal at the beginning of overtime, and especially in games with so much pressure and when fatigue sets in, it is difficult to come back.
“Having said all that, I am proud of our team and the strategy and vision we have for the club. We still have two cups to fight for in the remaining part of the season, and I think the quest to fight for this trophy will only make us better.”