The defender netted twice, with Fabio also on target, before the goalkeeper was forced to leave the pitch in the first of the country's four pre-World Cup friendlies
Layun found the net on either side of half-time and Marco Fabian added another as El Tri won the first of four friendlies before opening their World Cup campaign against Cameroon on June 13.
The Mexican Federation used the Israel match to celebrate the career of legendary forward Cuauhtemoc Blanco, who recently signed with Puebla at age 41 and wore the No. 10 shirt in more than 100 matches for his country.
Herrera named his starting line-up on Monday, surprisingly leaving Javier Hernandez on the bench. Instead, Blanco and Oribe Peralta started up front.
Many questioned the decision to hold a tribute match as Herrera's side began its final preparations before heading to Brazil. But Blanco did not bring the team down, setting up a scoring opportunity for Peralta in the 23rd minute and drawing a free kick from outside the box in the 34th before being subbed out.
Blanco was taken out of the game after just 39 minutes and handed the captain's armband to goalkeeper Jesus Corona. The second-leading scorer in Mexico national team history was replaced by Raul Jimenez.
Shortly before Blanco was given a ceremonial golden boot trophy and made a victory lap around the stadium in his final national team match at half-time, Layun scored his first career goal since making a Mexico roster for the first time a year ago.
In the 43rd minute, the defender cut inside from well outside the box and fired home a long-range bullet past the surprised goalkeeper Ariel Harush, who should have been able to make the save but played the wobbly ball very poorly.
Goal-scoring machine Hernandez came on at half-time for Peralta and the second half started much like the first, with Mexico controlling the match.
But once again, it was Layun to provide the offence for El Tri as he scored on another shot from distance. It appeared Harush had made a diving save but the ball took a bounce over the goal line, with Chicharito right there in case it didn't cross the line.
While fans were still celebrating the two-goal lead, Mexico were given quite a scare when Corona went down with an apparent neck injury caused by his own team-mate. The goalkeeper collided with Maza Rodriguez and he was stabilized and stretchered off, causing a stoppage in play for five minutes.
Guillermo Ochoa, who many believe is good enough to start for El Tri at the World Cup, was called upon in the 73rd minute and helped his team hold on for the clean sheet.
Fabian closed a strong performance by the home team after putting a deflected cross from Chicharito into the goal from the edge of the box in the 85th minute.
El Tri will play Nigeria this Saturday in Arlington, Texas.