Martinez, a 31-year-old midfielder who joined San Jose prior to this season, broke open a scoreless match in the 48th minute. The former Honduran international collected a ball from teammate Steven Lenhart, cut inside Seattle defender DeAndre Yedlin and fired from 12 yards.
Sounders emergency goalkeeper Andrew Weber, who came on at halftime for injured starter Michael Gspurning, could not keep the ball from curling inside the far post.
Weber, a former Earthquake, joined Seattle on loan from Phoenix FC of the USL Professional Division earlier this week after veteran backup Marcus Hahnemann was ruled out due to a hamstring injury.
San Jose (6-9-6) broke a two-match losing streak by posting just its second shutout of the season. Without leading scorer Obafemi Martins, out because of a calf problem, Seattle's offense generated just one shot on goal an easily saved 83rd-minute header from Eddie Johnson.
Weber kept Seattle (7-7-3) in the match with a one-on-one save against Lenhart in the 54th minute, but the Sounders couldn't take advantage and fell to .500 for the first time since May 26.
After a Seattle free kick in the 94th minute was snuffed out by San Jose's wall, Sounders midfielder Osvaldo Alonso was shown a straight red card after jostling with Quakes defender Dan Gargan.
Seattle had to use all three of its substitutions on injuries. In addition to Weber replacing Gspurning, midfielder Brad Evans went out with bruised ribs in the 32nd minute and defender Djimi Traore was replaced in the 53rd after several hard collisions.
Gspurning helped keep the match scoreless with a diving stop in the 14th minute to stop what would have been a spectacular goal from Martinez, who let fly with a strong right-footed bicycle attempt from the penalty spot.
Four minutes later, Gspurning scrambled to intercept a header from Alan Gordon, who was looking to cut Martinez's left-wing cross against the grain to the back post. Gspurning appeared to injure his left wrist on the play when Lenhart caught him with a late challenge.