It was the 17-year-old's first appearance for Arsenal since being stretchered off after 35 minutes of January's Fourth-Round tie against Wolves with a fractured ankle.
Murphy is rated a big prospect at Arsenal and told the club's website: "It's great to be back because it's frustrating watching, you want to be part of it.
"Thankfully it all went well when I got the nod, I got the goal, but more importantly we went through. The team did great today.
"In football you have to take the good with the bad and the physios are great at keeping you focused. I've been working closely with Cookie [Jon Cooke - Youth Team Physiotherapist] and Craig [Craig Gant - Youth Team Fitness Coach] who have been great - although they have made sure I give them a special thanks!
"There's no good time to be injured but hopefully you get them out of the way. No player wants to get injured but it makes you sure you can come back from them - although I never have any doubt."