The versatile Melbourne Rebels back injured his sternum in the 20th minute of the 36-32 loss to the Auckland Blues at Eden Park and received treatment on the field.
A few minutes later, the 22-year-old was forced to tackle burly Blues centre Rene Ranger head-on and immediately left the field for good, stretching his neck as he walked down the tunnel.
O'Connor, who missed much of the last international season with liver and hamstring injuries, tweeted that he was going to get an MRI scan and an X-ray on the injury and hoped there was no internal damage.
"Painful stuff! popped my sternum out on that kick receipt then didn't help when I got back up & had ranger with a 40m run up coming at me," he added.
Kurtley Beale, another candidate for Australia's number 10 shirt for the three Lions tests in June and July, missed the match for a breach of discipline after Melbourne's game last week and could yet face sanctions from the Australian Rugby Union.
Quade Cooper, who was first choice fly-half until he injured his knee at the 2011 World Cup, looked back close to his best in tandem with Wallabies scrum-half Will Genia for the Queensland Reds on Friday.
The New Zealand-born playmaker fell out with Deans in spectacular fashion last year, however, and was omitted from a 30-strong planning squad for the Lions series that assembled in Sydney last month.
Even if he was not selected at fly-half, O'Connor remains one of his country's most dangerous backline players, not to mention a reliable clutch kicker, and would be a certain starter against the Lions.
Wallabies coach Robbie Deans will name his first 25-man squad for the series next weekend with a further six players to be added on June 11.
After having to cope with a lengthy injury list last season, Deans has had better luck this year even if outstanding open-side flanker David Pocock has been lost for the season to a serious knee injury.
The Lions play the Barbarians in Hong Kong on June 1 and arrive in Australia the following day.
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