The talented teens were leading their tables in the U/18 girls and U/14 boys sections after two of three finals heats.
The third and final round was to have been held at Bells Beach this month, but was cancelled due to the COVID-19 pandemic.
Naylor took out heat one and posted a third in the second heat for an end of season tally of 1730 points.
Point Lonsdale's Minnie Vorath finished in third place in the age group.
Phipps ended the season with a commanding 2000 points, having won both heat finals.
"It feels so great to finish up on top especially for my last year in the juniors," said Naylor. "Hopefully comps will resume soon. We find out on the 14th of September whether the Australian Titles will go ahead."
The Woolworths Victorian Junior Surfing Titles is the exclusive qualification pathway for the State's elite junior competitors for selection into the Victorian Junior Surfing Team, set to compete at the Australian Junior Surfing Titles later in the year.