Robbie Thomson pushed away Waghorn's 89th-minute spot-kick but Rangers soon worked a short corner to Nathan Oduwa, who crossed for Waghorn to head home for a 2-1 victory and preserve the Ladbrokes Championship leaders' perfect league record.
The English striker told his club's official website: "It was a roller-coaster of emotions for me, from the disappointment of the penalty to the winning goal.
"But the character of the lads to keep going and get the win makes it that bit more satisfying.
"I was disappointed because it's not nice to miss so close to the end of the game but I just had to get on with the game. There is no point dwelling on it too long and letting it affect me.
"I found myself just running about to get it out of my head, so it was a relief that I got the chance at the end to make amends.
"The way it worked out it actually felt better winning it with the header than if I had scored the penalty.
"I just thought I would get through to the final whistle and see what happens, so it was pleasing to eventually get on the end of Nathan's cross and get the win."
Rangers trailed at the interval after failing to capitalise on large swathes of possession and allowing Derek Lyle to tap home from close range following a 35th-minute corner.
But they started the second half strongly and Jason Holt levelled with an angled finish in the 53rd minute.
The hosts continued to create chances and Waghorn felt the manner of their win was even more enjoyable than some of their more comfortable victories this term.
"The way we won it was more satisfying and to come back from a goal down was nice," he said.
"It's the first time we have been behind (in the league) this season, so it was great desire and work-rate from the boys to keep going right until the end."
Queens boss James Fowler was proud of the young players who came into the team and almost held out despite losing defenders Darren Brownlie and Lewis Kidd to injury 24 hours before the game.
Fowler said: "Scott Hooper who came in has not had much game time but to come to Ibrox and defend the way he did is a credit to him.
"Kyle Jacobs has played out of position at right-back but that has allowed Jake Pickard to come into midfield and he was excellent. Aidan Smith up top has quality and Liam Coogans came on at the end.
"That was a lot of young players and it's great experience for them but it will be sore for a day or two that we have not picked up any points."
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