The Rugby Park side are chasing a Scottish Premier League top-six finish and a win against the Buddies would have put them within touching distance of their aim.
But after Kris Boyd grabbed his first Kilmarnock goal in eight years to cancel out Esmael Goncalves' opener for the Buddies, they failed to find a winner and had to settle for a 1-1 draw.
A win at home to Dundee on Saturday would still be enough to see Kilmarnock into the upper half of the table but Shiels insisted the result against Danny Lennon's Scottish League Cup winners was not to be sniffed at.
He said: "We did exceptionally well against a team who, if we do make it into the top six, we won't find a harder opponent than.
"They have got quality right through the team and people have to start recognising teams like St Mirren.
"If they can keep their team together they have got a great chance of making Europe next season. I'm really impressed with St Mirren and I'm glad we were able to match them.
"In the second half we looked the more likely side to score. I don't know if their goal was offside but that is not relevant now."