The New York City striker returned to appear with Spain after replacing Isco Alarcon in the final minutes of the match against Italy.
La Roja continued to dominate throughout the first and they managed to bag a fourth goal five minutes before the break as Silva fired home a fine free-kick.
The game was all but wrapped up a minute later when Isco fired home but there was to be no let-up from Spain.
The Chelsea striker tucked his header away, followed by a horrendous defensive error that allowed Isco to slot the ball home.
Italy's victory over Israel means Spain's lead over the Azzurri remains at three points with two matches to play.
Ethan Ampadu was an unused sub as Wales won 2-0 in Moldova.
Morata gained a starting place for Spain as Marco Asensio was relegated to the bench.
Only the nine group winners automatically advance from European qualifying, with the eight best runners-up going to a playoff round.
INPHO Ryan Byrne
Serbia is similarly in control of Group D after beating Ireland 1-0 to go four points clear.
Two points now separate the top four sides in Group I.
"At the end of the day the important thing is we have three more points and are a little step closer".
Mario Pasalic was also an unused sub for a Croatia side beaten 1-0 in Turkey.
South Korea's point was enough to earn automatic qualification while in Group B a second half Saudi Arabia winner over Japan sent them through alongside their already-qualified opponents.
Austria drew 1-1 at home to Georgia.
Spain were four up at half-time via David Silva's 41st-minute effort, before sub Aspas netted twice either side of Morata's second goal.
Iago Aspas says that his close friendship with Spain teammate Alvaro Morata helps the pair thrive while playing together.