His fellow international Kurtley Beale chipped in with a first-half interception try and Gareth Delve also touched down.
However, it was a passionate performance from the entire Rebels team that enabled the team who finished bottom last year to edge the three-times champions.
The Rebels folded after going behind early in the second half against the Otago Highlanders last week but on Thursday showed great character to battle back into the lead - even if skipper Delve's last-minute try inflated the scoreline.
"It was another real nailbiter, a bit closer than we'd have liked," the Welsh number eight said in a pitchside interview.
"We're still a young team and looking to develop and that was another big step forward. The way we stuck together shows how we're coming together as a side."
Tries from fullback Rudi Wulf and flanker Chris Lowrey three minutes from time could not save the Blues from a fifth defeat in six matches this year and they will remain rooted to the bottom of the competitive New Zealand conference.
With the teams having just two wins between them a third of the way through the season, it was never likely to be a classic encounter and there were plenty of errors on both sides throughout the evening.
The first of any significance was the attempt of Blues number eight Brad Mika to force a pass out wide in the 11th minute and he paid a heavy price when Beale moved up to snatch the ball before racing the length of the pitch to score.
O'Connor had already kicked a penalty and added a second after 17 minutes which, set against young Blues fly-half Gareth Anscombe's three penalties, sent the home side into the break 11-9 up.
When the Blues backline finally managed to get the ball out wide without a forward pass or handling error to allow Wulf to get over the tryline three minutes after the break, it looked like the visitors might run away with the match.
O'Connor, however, put the Rebels back in front with two more penalties and when impressive replacement hooker Ged Robinson sent him in for a try after 65 minutes, they had enough of a cushion to survive a late onslaught from the Blues.