Sissons followed 45 seconds down on the leaders in the large chase group that included Mario Mola (ESP), Richard Murray (SAF) and Laurent Vidal (FRA).
Gomez and Jonny Brownlee then ran side by side throughout the 10km, putting on a stunning display of racing, and it was Gomez who won in a sprint finish to claim line honours and the overall series title.
Alistair Brownlee meanwhile was consigned to urging his brother on whenever they passed on the course, suffering from an Achilles injury that saw him limp to the finish.
For the Kiwis, Sissons ran through a number of athletes to finish 22nd and Dodds came 37th after emptying the tank on the bike and having to overcome the puncture. Martin van Barneveld withdrew early on the bike leg after losing too much time in the swim.
Sissons reviewed what was a fast race in tough and testing conditions.
"I have been struggling with the swim this season and today was the same, I was in a decent pack [on the bike] and we worked hard to catch up to the main pack, the goal was to get as close to the front as possible and we managed to do that but it took a good bit of energy to do that, we were chasing for a good 30k,'' he said.
"I was a little bit cold to begin with but then you started to warm up pretty quick, we were lucky the rain stayed away for the majority of the bike, that is where you get coldest, on the run you warm up pretty quickly on the run.''
Sissons ends the year ranked 13 in the world, with Dodds 41st and Clark Ellice, who did not race in London, at 34 in the world.