With the match finely poised at 2-1 to the Buddies, Adam Brooks was smacked on the face by Alex Gogic’s arm inside the box.
But referee Ryan Lee waved away the protests from the Palmy faithful and the top flight side marched up the park to score a killer third and knock Queens out of the cup.
Murphy said: “It’s really frustrating. Looking back at the footage, Adam cuts inside and Gogic puts his forearm up and he connects with his face. I would be screaming for it and if it was given against me I wouldn’t have any arguments.
“It’s clever defending from an experienced defender. We’re not going to argue about it now. It is what it is now.”
The Doonhamers knew they would have to be at their best to match their Prem opponents. But Murphy’s pre-match plea of keeping it tight for the first 10 minutes failed to materialise when the Buddies opened the scoring early doors.
A long-throw into the Queens box wasn’t properly cleared by home defender Jack Brydon and Olusanya nipped in at the back post to tap in on 10 minutes.
And the forward got his second 11 minutes later. Callum Penman’s terrific delivery found Olusanya who powered his header past a full-stretched Ross Stewart.
The cup tie could’ve been all-but over on the half hour mark when Michael Mandron’s sensational overhead looked to be heading into the top bin but Stewart produced a remarkable save to turn the ball behind.
Just before the break Queens had a big chance to halve the deficit when left back Oscar MacIntyre whipped in a brilliant cross that found Mikey Hewitt but his close range header was straight at the keeper.
Queens’ cup hopes were back on when Brennan Dickenson buried a first-time strike into the bottom corner on 75 minutes to set up a grandstand finish.
The Palmerston faithful were screaming for a penalty deep into injury time when Gogic bundled down Brooks inside the box but ref Lee was unmoved.
And Stephen Robinson’s men finally put the tie to bed seconds later after a quick breakaway resulted in Caolan Boyd-Munce firing into the top corner.
Murphy was proud of his players’ efforts, and said: “I thought we were excellent throughout the whole game.
“We’re a League One side against a top five Premiership club. We passed the ball and played really well we had threats but we’re really disappointed to give away two goals from long throw-ins.
“But if we’re going to go out of the cup, that’s the way to go out.
“I think the way our players were playing, I think we all believed. We kept going in the second half.
“When it did come together and we got up the park we made a couple of chances and scored a great goal.
“The tie was alive and our players believed and we pushed bodies up the park to try get back level.
“Unfortunately we made a mistake in midfield for the last goal. It was a counter attack.
“We now move onto a big match against Inverness on Tuesday night.”