But it was far from plain sailing for David Moyes' side that needed a late Victor Anichebe goal to finally see off the gallant Greek side.
Larissa had beaten Blackburn in the first round and started well as Everton struggled at first.
But in the 14th minute the deadlock was broken when Cahill, who had been sidelined since March, headed Leon Osman's driven cross home.
Elias Kiriakidis saw a long-range effort sail over the bar while James McFadden went close to doubling Everton's lead as Moyes' side began to dominate.
Former Everton striker Ibrahima Bakayoko had a 33rd minute effort easily gathered by Tim Howard before Cahill's 25-yard effort four minutes before the interval was saved by Stefanos Kotsolis.
Immediately after the restart Joleon Lescott broke up a Larissa attack and sent McFadden clear but the former Motherwell man saw his effort blocked by Kotsolis when he should really have scored.
Everton doubled their lead in the 50th minute with a superb goal, Osman smashing a thunderbolt home after good one-touch play by Leighton Baines and Steven Pienaar.
However, Larissa pulled a goal back in the 65th minute when Howard and Lescott got in a muddle and Cleiton profited from the lapse to make it 2-1.
The Greek side pressed for an equaliser but Everton's win was confirmed when Thomas Gravesen headed the ball through to Anichebe who coolly restored Everton's two-goal advantage.