South Africa found themselves 19-7 down after 31 minutes in the first half, but ultimately outscored Japan by eight tries to three.
And Theron admits that the first half was a bit of a shock to him and his team.
He says: “The first half was a bit of a shock for the guys and I think they didn’t really expect that.
“But I told [the players] that this is a World Cup, you have to convert your opportunities into points.
“We probably were a little shell-shocked when they scored those three tries, but I am proud of the way the players fought back.
“Japan played well and they targeted the rucks, which they did not do last year.
“It was a tough lesson for us, but we adapted quickly.
“I think we regrouped very well as a team after a hard team talk at half time and we stuck to our structures, which worked in the end.”
Powerful flank Zain Davids won the Man of the Match award after scoring two tries for the Bokkies.