The West Australian came into the day in 41st overall, 1 minute and 26 seconds back from yellow jersey holder Wout van Aert (Jumbo-Visma), O'Connor finishing with the peloton in Stage 4 as the Dutchman raced to a solo win.
And as the riders began the treacherous journey through the cobbled sectors of Stage 5, O'Connor's survival plan seemed to be going well given the circumstances, until he fell victim to a puncture on the second cobbled sector with 50 kilometres to go.
"I was on the second sector and I punctured," O'Connor told SBS following the stage.
"Then the race started to split a lot and it was really hard to chase back, there was a million cars inbetween and too many motorbikes and TV cameras.
"So it was a bit rough for us to chase and we could never really get close."
He got back on the bike and his AG2R Citroen teammates swiftly dropped back to support before O'Connor took the chase into his own hands on the cobbled section of Émerchicourt à Monchécourt, trying to close a minute's gap to a peloton containing most of the overall favourites.
Unfortunately, his efforts were in vain, as the pace ahead quickened with the peloton trying to catch a two-man attack made up of Tadej Pogačar (UAE Team Emirates) and Jasper Stuyven (Trek-Segafredo) from taking significant time.
While the race is far from over, time gaps looked to be a certainty amongst GC riders today and for O'Connor, he was caught on the wrong side of such gaps, the chance at a podium in Paris looking far from likely with such a big overall deficit.
While his puncture happened on the cobbles, O'Connor surprisingly revealed he didn't think the gruelling pavé was his undoing on the day, and put it more down to plain bad luck.
"It wasn't the cobbles, I honestly can't lie," he said.
"It's just really bad luck. I'm a bit sad and a bit disappointed.
"I feel calm for once because it's been a stressful couple of days, but I'm a bit sad because there wasn't much else I could've done today."
O'Connor will now be hoping he can use his climbing prowess to make up some time once the race enters the mountains in Stage 7, the finishing ascent to La Super Blanche Des Belles Filles one that could see more splits like those caused by today's brutal cobbles.
While Simon Clarke (Israel Premier-Tech) headlined the Australian efforts with a gutsy stage win from the breakaway, Jack Haig (Bahrain Victorious) and Caleb Ewan (Lotto Soudal) had similar days to O'Connor.
Both Haig and Ewan fell victim to a crash caused by a hay bale on the road with 30 kilometres to go. Riding well prior to the incident, Ewan was able to get back on the bike and cross the finish, but Haig experienced another cruel twist in his Tour de France journey as he was unable to continue, shades of his early exit after last year's Stage 3 with a broken collarbone an all too familiar memory.
The Tour de France continues with a hilly Stage 6 over 219.9 kilometres from Binche to Longwy. Watch on SBS, SBS On Demand and the SBS ŠKODA Tour Tracker.
