The defeat saw Italy finish bottom in Group C, while Scotland progressed as a result and will face New Zealand in the last eight.
Second-half tries from Willie Manu, Daniel Foster and Peni Terepo were enough to win the match for Tonga, with Samisoni Langi converting one and also kicking a penalty.
MORE: Have Australia hit their straps at Rugby League World Cup? | Stephen Kearney pleased with New Zealand win
However, Tonga's second victory of the tournament was not enough to send them through to the knockout stages.
Meanwhile, the Cook Islands registered their first 2013 Rugby League World Cup triumph, defeating Wales 28-24 in their final group game.
Both sides ran in five tries during the clash in Neath, but the reliable kicking of Christopher Taripo sealed the win for the Cook Islands.
Wales found themselves 16-4 down at half-time following scores from Daniel Fepuleai, Keith Lulia and Isaac John.
The hosts produced a fine second-half comeback but it was all in vain as the Cook Islands held on for the win.
Neither side could qualify for the quarter-finals as the USA had already secured top spot in Group D.