Spain shrugged off a rash of injuries and sickness to key players, including Xavi, Fernando Torres and Xabi Alonso, and easily dominated the ultra-defensive visitors in the Group I match in coach Vicente del Bosque's home town of Salamanca.
Striker David Villa, who needs one goal to equal Raul's Spain scoring record of 44, and defender Sergio Ramos both hit the post in the first half before Llorente struck two minutes after the break, leaping to nod in a Ramos cross.
The visitors hit back through Darvydas Sernas in the 54th and Santi Cazorla provided the centre for the powerful Llorente to put Spain back in front two minutes later.
Silva, who was lively throughout at a packed Helmantico stadium, made it 3-1 in the 79th with another header, sending a Ramos cross whistling into the top corner from the middle of the penalty area.
"These were three very important points for us," Del Bosque said in a television interview.
"We lacked shape in the first half but we improved and we were deserved winners."
POLICE CLASHES
Victory in their first home game since winning the World Cup in July put Spain top of Group I on six points from two matches following last month's 4-0 win in Liechtenstein.
The Lithuanian players were clearly under orders to sit back and try to catch Spain on the break and the home side had to wait until the 12th minute for their first real opening.
Silva found space on the right of the penalty area and stung the hands of goalkeeper Zydrunas Karcemarskas with a fierce drive.
Ramos almost gave Spain the lead in the 21st when he met Andres Iniesta's corner but his header bounced back off a post.
Lithuania had a rare chance four minutes before the break but Tomas Danilevicius's shot was straight at Iker Casillas and the Spain captain palmed the ball away.
Immediately after, an out-of-sorts Villa somehow failed to find the target with the goal at his mercy and Karcemarskas stranded but his shot from just to the right of the goal shaved the outside of the left upright.
Del Bosque threw on Aritz Aduriz and Pablo Hernandez in place of Villa and Llorente with just over 10 minutes left, Aduriz winning his first cap, and both substitutes went close to extending Spain's lead.
The match was marred by clashes between a handful of Lithuania supporters and local police at the start of the second half.
Officers used batons to subdue some of the visiting fans and the trouble quickly subsided without delaying the game.
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