Barnes, who is on the coaching staff at the Wild Knights, helped devise a plan which saw the Spears' Australian playmaker bottled up for much of the League One game, unable to impose himself as last year's beaten finalists surrendered top spot on the point's table after theirsecond loss of the season.
Featuring the Aussie-schooled Brave Blossoms trio of centre Dylan Riley and backrowers Jack Cornelsen and Ben Gunter, the Wild Knights led 15-10 at halftime but appeared to have blown it after the Spears scored 17 of the next 20 points to lead by nine with 11 minutesremaining.
Two tries brought Saitama back into the equation before Brave Blossoms flyhalf Takuya Yamasawa cooly converted fullback Ryuji Noguchi's 83rd minute score from near touch to secure the spoils.
Saturday's result allowed Dave Rennie's Kobe Steelers to climb to the top of the standings, battering Sagamihara Dynaboars 61-10 to complete a memorable two weeks for the ex-Wallaby boss, after he was last month unveiled as All Blacks coach.
The playoffs hopes of Semi Radradra's Shizuoka BlueRevs grow more tenuous by the week. They slumped to their fifth defeat in a row when All Black scrumhalf TJ Perenara scored in the 79th minute to hand BlackRams Tokyo a 37-33 win.
Bottom placed Yokohama Eagles claimed their second win, beating Mie Heat 31-26.
Elsewhere, Wallaby veteran Sean McMahon's Tokyo Sungoliath took the bragging rights in the city's west, crushing Brave Lupus 60-21 in Sunday's Fuchu derby.
The win was fourth-placed Sungoliath's first in three years against their local rival.
Urayasu D-Rocks are winless in their past seven, outclassed 59-19 by Steve Hansen's rejuvenated Verblitz.
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