The City playmaker came on as a 52nd-minute substitute and took just 17 minutes to get on the scoresheet.
Gerard Deulofeu was brought down in the box and it was Silva who stepped up to stoke home the resulting penalty – his 30th goal for his country – he is now just eight goals behind third-placed Fernando Torres.
Silva’s presence changed Spain’s approach and there was a more fluent look about La Roja after his introduction.
As ever, he has an understated but crucial role in Spain’s second goal as he played the ball to Jordi Albi who crossed for Deulofeu to prod home at the far post.
Silva came close to scoring a second in the dying minutes, side-footing a shot wide when well-placed.
With 111 caps won, Silva is now just three caps behind sixth-placed Xabi Alonso in seventh spot for Spain’s all-time cap-winners.
With 30 goals, he is fourth highest scorer for his country.
Sergio Aguero was also a second-half sub as Argentina suffered a damaging 2-0 defeat to Bolivia in La Paz.
Kun replaced Correa on 56 minutes but the hosts were already two goals to the good - Argentina now face a battle to qualify with just four qualifying games to go.
Fernandinho was an unused sub in Brazil’s 3-0 win over Paraguay - a victory that all-but seals qualification for next summer’s World Cup in Russia.
There was better news for Claudio Bravo as Chile beat bottom side Venezuela 3-1 in Santiago. The Chileans were 3-0 up after just 22 minutes and now move above Argentina into the fourth qualifying spot.
