The legendary Brazilian converted from the spot in the 14th minute, with Thaciano adding a second and Guilherme sealing the win with his 70th-minute strike after an assist from Neymar.
Neymar's last goal came in October 2023 for Al Hilal. A serious knee injury restricted him to only seven appearances after joining the Saudi side in 2023.
"I'm happy to be playing again. I feel I'm improving," he said. "Obviously I'm not going to be 100% physically, it's only my fourth game but I'm getting better and better.
"I was anxious to score and wanted to dedicate this to the fans and my family."
Neymar began his career aged 17 with Santos in 2009, racking up 136 goals and 64 assists in 225 matches to help the club secure their first Copa Libertadores title in nearly 50 years in 2011.
He joined Barcelona in 2013, moved to Paris Saint-Germain for a world record fee of 222 million euros ($232 million) in August 2017 before joining Al Hilal for a reported fee of around 90 million euros.
Brazilian media has reported that Neymar's deal with Santos runs until the end of June.
"We're helping each other, Santos are helping me, they've opened doors for me to rediscover soccer, to rediscover joy," Neymar said when asked about extending the contract.
"I didn't want to sign a long contract because I didn't know how I was going to come back. I didn't know how I was going to feel during these months. Let's enjoy these moments, its the start of a great era for Santos."
Santos next host Noroeste in the Paulista on Wednesday.