The 18-year-old came on for England international Emile Smith-Rowe with 10 minutes to go, and found the net in the final moments, sliding home Nicolas Pepe's cross.
Patino left Kenilworth Road for the Gunners back in May 2015, aged just 11, for a fee reported to be over £10,000 at the time.
He has since gone on to impress for the various age-groups at the Premier League side, earning a host of England youth caps as well, signing his first pro contract last year.
Speaking to the official Arsenal website about Patino, boss Mikel Arteta said: "A beautiful moment.
"He is a kid that is coming through our system, a lovely kid.
"He is training with us almost every week.
"It was a dream. As a debut to come here, to score in front of our fans, a really special moment.
"They (supporters) heard about him and know what he can become and now we have to cook him slowly. Today was a good start, I think.
"That is what we have to avoid (hype).
"He still has a lot of competition in front of him. He is really young and he needs to go step by step.
"Today he was lucky, he got the opportunity and he took it really well."
Another former Hatter who went to the Gunners, Jack Wilshere, tweeted: "Hard work paying off, love it Charlie boy."