Maxence Lacroix's second Conference League goal of the season set Palace on their way not long before the break. And despite a few minor scares in the second-half, Evann Guessand wrapped up the game late on with a fine finish.
Henderson wasn't overly busy but gave a solid display as he racked up a century of appearances for the Eagles.
But after Palace's passage to the Round of 16, he was full of praise for his teammates for an accomplished display in front of him.
"Obviously, the lads did the job," he told TNT Sports. "They were fantastic, and I knew we'd get a good reaction.
"As the manager said it's three in six [clean sheets]. And we've got to get back to that.