Botes was forced off in the 34th minute as Sipho Senne took the striker's place at Royal Bafokeng Stadium on Saturday.
Dikwena were undone by goals either side of the break from Rhulani Manzini and Menzi Masuku in Rustenburg.
“It did change a lot because Henrico gives you the effort upfront,” Johnson told the club's website. “He gives you the effort especially in the fact that he brings in all the other players into play. There’s no way he is going to give up in a tackle. He gets in and gets up and carries on again. We lost that bit of effort in the game.”
The former SuperSport United boss hopes to keep his men active in the FIFA break ahead of Stars' next league clash with Kaizer Chiefs at FNB Stadium on September 14.
“It’s a bad break. You have got to stay in the competition to stay active. We have got to find different ways of playing now in order to stay competitive. If we do that we will be okay when we play against Kaizer Chiefs in two weeks' time.”
He added: “They are professionals. They have to come to the fore and say you know what if I did x, y and z, I would have been better. Hopefully we are able to get it right and shine against Chiefs.”