Martin passed Freeman McNeil to become the Jets' all-time leading rusher with 8,185 career yards in a New York uniform.
Chad Pennington went 22-of-29 for 258 yards with two touchdowns for the Jets (2-0), who opened up a season with two straight victories for the first time since 2000.
LaDainian Tomlinson rushed for 87 yards with a touchdown for the Chargers (1-1).
Drew Brees had a tough game for San Diego as he completed only 8-of-19 for 146 yards with a touchdown, two interceptions and a fumble.
Doug Flutie came on in the final minutes and went 7-of-16 for 77 yards and ran for a score for the Chargers.