DeJon Gomes and Rickey Thenarse each ran back interceptions for touchdowns as the defense carried the day for the Huskers (2-0), whose offense was productive but mistake-prone against the overmatched Vandals (1-1).
Martinez went over 100 yards for the second straight game and Roy Helu Jr. added 107 yards and a touchdown for Nebraska.
The Huskers' Blackshirt defense made it a brutal day for Enderle, who grew up rooting for the Huskers and was playing in his home state for the first time since high school.
The fifth-year senior from North Platte was sacked five times, and he threw three of his five interceptions on consecutive possessions in the second quarter. Nebraska converted each of those second-quarter picks into touchdowns to go up 31-3 at half.
Helu scored from 58 yards the play after P.J. Smith pulled in a pass tipped high by teammate Prince Amukamara.
Gomes jumped in front of a ball intended for Maurice Shaw and took it 40 yards to the end zone for a 24-0 lead, and Thenarse followed with a 47-yard return after he swiped another pass meant for Shaw.
The Vandals couldn't run up the middle against Nebraska's front four, and they couldn't make the corner when they tried to go outside against the faster Huskers.
Enderle was 16 for 31 for 141 yards and was pulled midway through the fourth quarter after throwing his fifth interception to Alfonzo Dennard.
Brian Reader came in and was sacked twice before he put together a 10-play, 98-yard TD drive against Nebraska's backups.
Idaho's other points came on Trey Farquhar's 34-yard field goal and Enderle's 2-yard touchdown pass to Michael LaGrone.
Martinez, who was impressive last week against Western Kentucky in his first start, showed again how dangerous he is on the zone-read option.
He scored from 67 yards after pulling the ball out of Helu's belly, heading right and making a fast left between his guard and tackle before accelerating in open field.
Martinez's second TD came from 20 yards after he had a 38-yarder erased by a holding penalty far behind the play.
That holding penalty on Brandon Kinnie was symptomatic of the Huskers' uneven offensive performance.
As good as Martinez was on the run, he seemed hesitant in the passing game. He fumbled as he got sacked, killing a drive after the Huskers had moved inside the Idaho 10. Later, he threw an interception that resulted in Idaho's first touchdown.
Nebraska's first possession was marred by a clip and an unnecessary roughness penalty. Another drive stalled after a false start and a clip left Nebraska with a first-and-30.
Receiver Niles Paul fumbled when he took a direct snap on the first play of the third quarter, and Dontrayevous Robinson fumbled at the Idaho 1 in the fourth.