Henderson put on a stunning show of power in the final metres of the 207km second stage of the Tour, from Vise to Tournai in Belgium, when leading out Lotto-Belisol teammate Andre Greipel in the final sprint, only to see Brit Cavendish sneak around the German to chalk up his 21st stage victory in the famous race.
Greipel finished second, with Australian Matt Goss third. Henderson, who coasted home after his flat-out effort, finished 26th.
It was an impressive effort from the New Zealander, who did well to feature in the high-speed finish and deliver his man a perfect lead out with 250m to go.
"Sometimes you get beaten by someone faster on the day. It happens. It's life. Congrats @MarkCavendish," Henderson tweeted afterwards, adding: "As for @Lotto-Belisol. We were all at the right place at the right moment. Our victory will come."
Henderson showed a glimpse of his form in the prologue when finishing 23rd of the 198 riders in the 6.4km time trial, but fell off the pace in the first stage, a 198km haul from Liege to Seraing which featured several hill climbs, including a tough one at the finish.
Swiss Fabian Cancellara continues to wear the yellow jersey after his stunning prologue victory, but it was world champion Cavendish who earned the most attention after his win in which he had to rely on his instincts rather than the usual help from his Sky teammates who had all dropped off the pace.
Cavendish, who described the win as one of his best, said: "I saw Henderson go on the left with Greipel on his wheel and I just moved left because when Hendy surged it kind of caught [Peter] Sagan by surprise and I was able to get on the wheel and then Greipel went. I even left it a bit late. I jumped off Greipel with about 200m to go, I should have gone a bit earlier because as you can see it was very tight for the line."
Tomorrow the race enters France for the first time in this edition of the race, with a tough 197km stage from Orchies to Boulogne-sur-Mer. It includes six big climbs, four of which are in the last 16km.