Michael Ngoo opened the scoring for the Reds before Adam Morgan rounded off the scores late on.
It was Liverpool who got off to the perfect start as they had a goal denied as early as the third minute.
Liverpool's Jordan Ibe was instrumental in the first half creating numerous chances for his strikers Morgan and Ngoo, many of these were wasted but Ngoo managed to find the back of the net with one to hand Liverpool a slender lead at the break.
Marseille came back into the match in the second half but showed a lack of composure on the ball and never really threatened to score.
Liverpool's captain Connor Coady and Hungarian midfielder Kristian Adorjan impressed in the second half.
The second goal came minutes from time when Morgan finally beat Marsielle goalkeeper Fabri to kill the game off.
Liverpool's Academy Director Frank McParland was pleased with his young teams performance during the campaign and is delighted with a third place finish.
He told reporters: "We are delighted with the result this afternoon - it was a very technical game, played in a fantastic spirit, and we are very happy to have finished third in such a magnificent tournament."