It said the US plane manufacturer, which is the arch-rival of Europe's Airbus, was given $5bn (Â£3.2bn, 3.8bn euros) in illegal government subsidies.
That is much less than the $18bn an earlier ruling found Airbus had received from the EU.
The WTO's appeals panel has now ruled on both sides of the dispute.
Each side claimed a partial victory.
The European Commission, which complained to the WTO, said it welcomed the confirmation of Boeing's subsidies, which it received between 1989 and 2006.
EU Trade Commissioner Karel De Guch called Monday's ruling vindication of the "EU's long-held claims that Boeing has received massive US government handouts in the past and continues to do so today".
His counterpart, US Trade Representative Ron Kirk, called the ruling "a tremendous victory for American manufacturers and workers".
Mr Kirk said US subsidies to Boeing cost Airbus 118 lost aircraft sales, while EU subsidies for Airbus cost Boeing 342 lost aircraft sales.
The subsidies included at least $2.6bn in assistance from the space agency Nasa, which the WTO's appellate body agreed had allowed the US company to launch its modern 787 Dreamliner, causing "serious prejudice" to its European rival.
The dispute between the two firms over state aid has been running for seven years.
The World Trade Organization (WTO) has upheld most of its ruling that Boeing received illegal subsidies from the US government.