Spain had already sealed their place in Russia as group winners and their only motivation was to keep up their slim chances of being seeded in December's World Cup draw, with the 2010 champions 11th in last month's world rankings.
Israel had long been out of contention for a playoff place, finishing fourth on 12 points, one behind Albania in third. Italy ended their campaign second on 23 points.
Coach Julen Lopetegui made nine changes from the Spain team that eased to a 3-0 win over Albania on Friday, with only Sergio Busquets, who made his 100th appearance for Spain, and captain Sergio Ramos keeping their places.
"We knew this was a difficult game for different reasons but we wanted to win and take another step towards recovering our winning mentality which could help us go on and win the World Cup," Spain goalkeeper Pepe Reina told reporters.
"If you had asked us before the campaign started, we would all have taken the results we got. Italy were the team to beat but every side posed their own difficulties and we've been very consistent, confident in ourselves and we've played in the style we wanted to wherever we've been."
Spain lacked the spark with which they had played their previous qualifiers, but still had the better of the chances and it took four impressive saves from Israel goalkeeper Ariel Harush to prevent the visitors leading before the interval.
Veteran forward Aritz Aduriz, youngster Marco Asensio and Ramos each saw long range efforts blocked, while the best chance of the half fell to Chelsea forward Pedro, who found himself clean through against Harush but scuffed his shot straight at the goalkeeper.
Athletic Bilbao striker Aduriz, 36, missed an even clearer chance early in the second half when he failed to connect with a rolling pass from close range, despite being unmarked.
It took another Basque player in Illarramendi to finally put Spain in front, while Asensio had a late strike ruled out for offside.
(Reporting by Richard Martin; Editing by Christian Radnedge)
