Imposing number eight Patrick Tuifua went blindside off the back of it and fended two defenders for his 20th-minute try.
Things went from bad to worse for St John's with openside flanker Tebs Tangau yellow carded for tackling the player receiving the kickoff in the air.
Lindisfarne had all the possession and territory over the next 10 minutes and eventually made it count on the scoreboard.
Openside flanker Kings Tupuola forced the ball loose with a big tackle, scooped it up and advanced towards the line.
Lindisfarne centre Corban Watson reached out to score a phase later in the 33rd minute.
There was time for another try before halftime too - Tuifua made a strong fend then offloaded to winger Hopa Keelan to make it 17-5 at the break.
The hosts came close to reducing the deficit with a strong spell to start the second half.
They were held up over the line once and had Lindisfarne on the back foot for the best part of 20 minutes after play resumed.
But player of the day Tuifua made the difference for his school once again, sparking a break and then finding Watson for a runaway try the other way to make it 24-5 with 15 minutes remaining.
Lindisfarne almost had a fifth soon after, but some brave goal-line defence from St John's held them out.
The hosts took the ball up the other end and had their chances to close the gap, but Lindisfarne held on despite a yellow card for lock Oliver Barham for repeated offside infringements.
Both teams have one more game to play in the Central North Island First XV round-robin.
St John's host St Peter's Cambridge on July 30 and Lindisfarne are away to Rathkeale on August 2.
