The powerful Athletic Bilbao forward, starting in place of the injured Fernando Torres, scored with two headers at the start of the second half to lead Vicente del Bosque's side to a 3-1 win which sent them two points clear at the top of Group I.
David Silva added a third header late on for the hosts to complete the scoring after Lithuania striker Darvydas Sernas had earlier netted a surprise equaliser for the visitors.
"I'm very happy, the game was difficult up until the goals, which were very important." Llorente, whose double took his tally to six goals for his country, told the Spanish press after the match.
"They (Lithuania) are a team who make things very difficult, but we've done a great job. The coach was right when he said that it would be complicated and now we need to turn our attention to Scotland, which will also be difficult," added the Spanish forward.
Llorente had ice placed on his ankle after being replaced in the 76th minute. "It's a blow from the last league match which I've been carrying since then," said the 23-year-old, "but I've finished well; tired for the big effort I've put in, but well."
Spain play Scotland in Glasgow on Tuesday, where they take a two-point lead over the Scots and Lithuania at the top of Group I.