Lin, who joined the Rockets from the New York Knicks in the summer, hit a career high 39 points with seven assists for Houston.
But Tony Parker recorded the first triple-double of his career with 27 points, 12 rebounds and 12 assists to secure the overtime victory against the Rockets, who were without guard James Harden because of a right ankle injury.
Gary Neal nailed seven three pointers and finished with 29 points for the Spurs, who have won five consecutive games.
Manu Ginobili finished with 22 points and six assists and Danny Green had 14 points and a half dozen rebounds.
Tim Duncan had a double-double with 10 points and 13 rebounds for San Antonio, which improved to 11-2 on the road this season.
Miami's LeBron James and Dwyane Wade went on a scoring spree to lift the Heat to a 101-92 victory over South-east rivals Atlanta on Monday, opening up a 1.5 game gap over the Hawks.
James tallied 27 points, seven rebounds and six assists, while Wade scored 26 points to snap Atlanta's three-game win streak and keep the Heat (14-5) ahead of the Hawks (12-6).
After a close first half, Miami trailed 65-63 in the third before seizing the momentum with a run of nine straight points. The Heat finished the stretch with a 14-2 advantage to open up a 10-point lead.
After two disappointing losses last week, the defending NBA champions have now won two straight.
Josh Smith scored 22 points for the Hawks, and Al Horford finished with 20 and 11 rebounds.
Stephen Curry returned to his hometown and put on a show the locals did not want to see, with his 27 points leading the Golden State Warriors to a 104-96 victory over the Charlotte Bobcats in North Carolina.
David Lee helped out with 25 points and 11 rebounds.
The Bobcats have now lost eight straight game.
A 31-3 run in the first half powered the Dallas Mavericks to a 119-96 win over the Sacramento Kings.
OJ Mayo led the Mavs with 19 points.
Jrue Holiday had 25 points to lead the Philadelphia 76ers to a 104-97 victory over the Detroit Pistons.
LaMarcus Aldridge had 30 points and 12 rebounds as the Portland Trail Blazers topped the Toronto Raptors 92-74.
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