Hodgson decided against playing Kane from the start but he grabbed England’s fourth goal on 72 minutes after Wayne Rooney, Danny Welbeck and Raheem Sterling had already found the net in a convincing showing from the hosts.
The goal was Rooney’s 47th for England and the striker is just two goals away from drawing level with Sir Bobby Charlton’s England goalscoring record, while Welbeck now has six goals in the qualifying stage meaning he’s the top scorer in the tournament.
The result leaves England six points ahead of Slovenia in Group E and stretches their unbeaten run in competitive matches at Wembley to 17.
Hodgson’s starting XI had got everyone talking in the build-up to the game with the possibility of Kane being handed a start, but the manager decided to go with his tried and tested attacking formula of Rooney playing central ahead of Welbeck and Sterling.
Hodgson’s decision was vindicated with an incisive first-half display.
Rooney had already hit the post from a Fabian Delph through ball when he gave his side the lead on six minutes.
Welbeck did the hard graft down the left, finding space to fire a shot that was parried into the path of Rooney, who nodded home from six yards.
The England striker could have drawn level with Gary Lineker in the all-time England scoring charts on 23 minutes but he planted a header against the crossbar from a Welbeck cross.
The Arsenal forward was the next England man to go close on 41 minutes, curling an effort wide of the upright after he showed a great change of pace.
He would eventually get his sixth goal of the qualifying phase just minutes later as he diverted a Jordan Henderson cross into the net via a big deflection off Marius Zaliukas.
The break for the half-time oranges couldn’t stop England’s fruitful attacking play and Delph forced Giedrius Arlauskis into a fine one-handed save with a crisp close-range volley on 50 minutes.
Welbeck was a constant menace down the right, showing various Lithuania defenders a clean pair of heels on many occasions, but he couldn’t add to his tally as Arlauskis denied him on 53 minutes.
The ball was in the net three minutes later when Sterling grabbed his first international goal after he turned home inside the six-yard box from a Rooney cross.
That was to be Rooney’s last major act in the game as Kane replaced him to great cheers from the home crowd on 70 minutes and that noise turned to delirium in the stands when he rose highest at the back post to head home a Sterling cross with just his second touch of the game.