Thanks to the efforts of his teammates Bernie Eisel, Tyler Farrar and Scott Thwaites, Janse van Rensburg sat tenth as they entered the final 3.5km lap.
Despite their hard work, it was the Quick-Step Floors team that took control as Marcel Kittel claimed the first win of the tour.
Bora-Hansgrohe’s Peter Sagan and Team Sky’s Elia Viviani completed the podium.
“It was a pretty fast day and with the annoying wind, it made it a bit nervous in the bunch as well,” said Janse van Rensberg.
“There were some fast laps to finish here at the end and the team did a super job to keep me in position.
“In the end, I did a little bit too much in the wind before the final sprint so I was already on the limit when coming to the line,” said the South African.
“Some of the best sprinters in the world are here so sixth place on a pretty fast day, I’ll take that for now but there are some better stages coming for me.”
Janse van Rensburg currently sits eight in the general classification after the first day.
The second stage features six King of the Mountain climbs and a short yet steep climb before the finish in San Jose, 144.5km after the start in Modesto.