Hearts picked up the three points thanks to goals from Gary Mackay-Steven and Stephen Kingsley after the interval.
St Mirren were the better side in the opening 45 minutes with Gordon producing heroics, as he did after the break with three important stops.
"The big frustration for me today is that at 0-0 we're the better team," Goodwin said. “I'm not saying we were miles better but I thought we were on top for the first 45 minutes, we pressed Hearts aggressively up the pitch, we played some good football and probably had the better opportunities.
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"Those key moments in the games are really coming back to bite us. Same last week against Livingston, we should have been two or three up and get done with a sucker punch in the last minute.
“Craig Gordon has to get credit, he’s a top, top keeper. He has made two or three saves that has kept Hearts in the game.
“Jak Alnwick has also made some really good saves.
“I don’t need to see the stats from the analyst.
“I thought it was a very even game at 0-0 and the first goal was always going to be huge. It was the manner of the way we conceded that first goal that hurts me.
“It’s a stupid, slow pass across the pitch that gets cut out. We didn’t get enough bodies behind the ball and the deflected cross just falls kindly for Mackay-Steven.
“It’s a decent finish but, unfortunately, we don’t seem to get these gifts at the moment and that’s the bit that’s hurting us.”
Goodwin was also left to rue a couple of decisions with Richard Tait having a goal ruled out for offside in the first-half and Joe Shaughnessy sent off late on for a challenge on Cammy Devlin.
"It looks very tight,” he said. “Unfortunately, the angle we have is too far away to give a definitive answer. You would like it to go in your favour but if the linesman has got it right then fair play to him – it's a hell of a call.
"I thought it was a great ball, a good run and a fantastic finish as well. We don't seem to get those decisions at the moment.
"I don't want to go on about it because I could say something stupid and Sportscene shows it was a brilliant decision. I haven't had the opportunity to see it properly.”
On the red card, he added: “I was disappointed. I can see why Alan Muir's come to that decision.
"Joe was last man and there is a bit of grappling on the edge of the box and you could argue if the Hearts player gets away then he has a free hit at goal but in the 95th minute when Hearts are 2-0 up and the game is done I don't think anybody would have minded if the referee had turned a blind eye to that one.”