The 33-year-old striker, who netted Real's third goal in a 3-0 win over Valencia in the 2000 final, scored just after the hour to cancel out a 17th-minute effort from another former Bernabeu favourite, Roberto Soldado.
His goal extended Raul's record tally in the three major European club competitions to 69 and came on his return to his native country after swapping La Liga for the Bundesliga at the end of last season.
"If it hadn't hurt us so much we would be the first to congratulate him," Valencia coach Unai Emery told a news conference.
"I think both teams deserved credit. Vicente Guaita made a lot of saves for us but in the end they managed to score. We also missed a lot of chances."
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Valencia controlled play for long periods at the Mestalla but squandered a number of openings and will be disappointed not to have converted their superiority into an advantage for next month's second leg.
Schalke will be without defender Lukas Schmitz for the return game in Gelsenkirchen after he was sent off for a second caution deep into stoppage time.
Raul and Soldado were two of four former Real players on the pitch, with Netherlands striker Klaas-Jan Huntelaar and German defender Christoph Metzelder also featuring for Schalke.
After a cautious start from both teams, Huntelaar fluffed a chance to put the visitors ahead when he failed to connect with an attempted close-range volley in the ninth minute.
It was Metzelder's mistake that led to Valencia taking the lead as he surrendered possession in a dangerous position and Jeremy Mathieu crossed for Soldado to clip the ball past keeper Manuel Neuer from six metres.
Raul, who spent 16 years in Real's first team, then found space inside the penalty area and drove a low, left-footed shot across keeper Guaita into the far corner of the net.
The veteran forward broke Gerd Mueller's 34-year-old European club competition record of 66 with a double against Hapoel Tel Aviv in the group stages in October.
Raul has scored his 69 goals in 137 Champions League matches while former German international Mueller needed just 74 games in the European Cup, Cup Winners' Cup and UEFA/Fairs Cup for his 66.
"He showed the class he has always had," Schalke coach Felix Magath said of Raul. "He exploited his talents, not only for the goal but all the work he put in during the match."
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