The decisive goal came after centre-back Mohamadou Sissoko attempted to control a high ball deep in his own area.
The subsequent clumsy touch allowed Francisco Sandaza to slide a pass through for Cillian Sheridan, who finished calmly.
But instead of chastising the defender, Shiels insists he will continue to encourage an expansive, risky style - even if it means Killie's league position suffers.
He said: "We have our philosophy, and we stay faithful to it. If that means us not progressing up the table then so be it.
"I've been down this road a lot. You have a footballing philosophy, where you tell your players to express themselves on the ball.
"My centre-half tries to bring the ball down and miscontrols it and it causes a goal. How can I criticise him when I tell him to do that?
"When Mixu [Paatelainen] and I were here we went on a period of losing four or five games on the bounce and people start to question you, and you've got to be strong.
"It would be hypocritical for me to start playing in a different way and I will not do that.
"I think in every game this season we have entertained the paying public.
"We haven't had any luck this week, and sometimes you get that in football. I think anyone that knows anything about the game would agree we deserved to win today."
Referring to his side being booed from the field, Shiels continued: "That's their frustration and I don't mind. They are in an emotional state of imbalance, as I am, after you lose a game of football."
Saints boss Derek McInnes, who saw his side take the lead through Sandaza before a Steven Anderson own-goal levelled matters, unsurprisingly disagreed with Shiels' frank assessment.
Indeed, the former Rangers midfielder believes the Perth side were the better side, and hailed the experience in his side which has helped facilitate away wins at Fir Park, Celtic Park and now Rugby Park this season.
He said: "Regardless of what has been said I think the better team won.
"We've got good experience in key areas of the pitch and that brings you a confidence in your defending.
"We were unlucky losing in midweek [3-2 defeat at Easter Road] to a penalty that was never a penalty, there was a real sense of injustice, so we came here determined to make up for it and get three points.
"Apart from a 15-minute spell when (James) Dayton, (Paul) Heffernan and (Dean) Shiels were all involved I thought we dealt with Kilmarnock well, and in the second half I thought we were comfortable."
Source: Team Talk
Source: Team Talk