The livewire 18-year-old was a constant source of threat for Rugby Park men as they beat relegated Dundee 3-2 in their penultimate Clydesdale Bank Premier League fixture.
He scored the visitors' second with a brilliant finish 13 minutes into the second half to put Killie ahead for the second time and could also have had a penalty after Dark Blues defender Kyle Benedictus barged him over in the box.
Referee Euan Norris waved away his claims while the home support claimed the youngster had gone down easy.
But Shiels was convinced his player had been fouled and demanded SPL officials show better care with his talented teen.
He said: "Chris Johnston is going to be hard to referee and they have to develop an understanding of a seven-stone player who has got a change of pace. When he beats people, he doesn't dive. Believe me.
"I was angry with the crowd (for jeering him). When he gets the ball, his mechanics and the way he changes direction so rapidly in that moment make him vulnerable. The slightest touch will send him down.
"He was fouled twice in the box but didn't get the penalty. Anywhere else on the pitch and it's a free-kick.
"Scottish supporters need a player like that, they are paying 20-odd quid to get into a game, so we have to protect him and I felt he wasn't protected. Once the referees like Euan get to know him, they will say, 'Wow, he's a good player, let's give him protection'."