The hefty sum is significantly less than the billion dollars Apple sought at the outset of the 2012 patent trial in Northern California, and doesn't put to rest an argument over who should pay Apple's legal costs said to total $1.8 million.
"Samsung has confirmed to Apple that it will pay Apple the $548 million partial judgment directly," lawyers representing the companies said in the court filing.
The payment was to be made within 10 days of Apple delivering an invoice to Samsung on Friday, according to a joint filing.
In another sign the long-running legal fight would drag on, Apple also asked the court for approval to file a motion asking for supplemental damages for products that weren't calculated into the award.
Arch-rivals Samsung and Apple decided last year to drop all patent disputes outside the US, marking a partial ceasefire in their long-running legal war.
The companies have battled in close to a dozen countries, with each accusing the other of infringing on various patents related to their flagship smartphone and tablet products.
But neither has managed to deliver a knock-out blow with rulings going different ways, and an announcement they agreed to drop all litigation outside the US suggested a line was finally being drawn.
However, the agreement came with one key caveat, with the two giants stressing they would continue "to pursue the existing cases in US courts".
