Spain coach Julen Lopetegui insisted he was satisfied after the 2-1 win in Macedonia.
The Spaniards stayed in control of Group G thanks to first-half goals from David Silva and Diego Costa.
However, they let Macedonia back into the game midway through the second half when Stefan Ristovski pulled a goal back.
Nevertheless, an unconvincing victory ensured Spain remain top on goal difference despite Italy's 5-0 win over Liechtenstein.
"The goal was to get the three points and we did,'' said Lopetegui at his postmatch news conference. "We are pleased with the collective performance.
"This is football at the highest level. If you do not take advantage of your chances, you can pay for it. But the assessment is positive.''
The visitors took the lead after 15 minutes following a classic Spanish build-up.
Andres Iniesta casually scooped the ball over the Macedonia back line to Jordi Alba, who pulled it back from the byline to Silva.
The Manchester City midfielder turned away from marker Vance Sikov before slipping the ball past wrong-footed goalkeeper Stole Dimitrievski and into the net.
The second arrived in the 27th minute thanks to a piece of brilliance from Isco.
The Real Madrid winger cut in from the right, jinking past two Macedonia defenders before squaring to the far post where Silva and Costa were queuing up for a tap-in.
Costa, who claims Chelsea coach Antonio Conte has told him he is not part of his plans next season, took the opportunity to put himself in the shop window by applying the finish.
But with chances going begging Spain were made to pay when, out of nothing, Ristovski burst from the halfway line to score his first international goal and ensure a nervy finale.
Italy and Spain drew 1-1 in Turin in October, and the pivotal return fixture is next up, in Madrid in September.
"I expect a great atmosphere against Italy at the Bernabeu and I'm sure that the fans will support us,'' added Lopetegui.