Andrew Rossig, 34, and James Brady, 33, were convicted of reckless endangerment and unauthorised climbing in connection with the jump in September 2013.
They were fined $2,000 (£1,285) each on Monday and given community service.
The pair leapt from the top of the 104-storey skyscraper after sneaking through a hole in a construction fence.
A third jumper, Marko Markovich, will be sentenced on 17 August.
Base jumping is an extreme sport, which involves leaping from high structures with a parachute.
The jumpers filmed their night-time exploits at One World Trade Center using helmet cameras and posted the video online.
It contains a museum and memorial garden dedicated to those who died.
Judge Juan Merchan said: “These defendants tarnished the building before it even opened and sullied the memories of those who jumped on 9/11, not for sport but because they had to.”
In June, a jury acquitted each of the three men of the more serious charge of burglary.
Speaking after sentencing, Rossig apologised for his actions and vowed never to parachute in New York City again.
“We understand that what we did could possibly have endangered other people and it’s never going to happen again,” he added.