Barnes, who linked up brilliantly with O'Connor when Australia beat Wales in Cardiff in December, accidentally kneed the youngster in the rib area in an aerial collision during the Waratahs' Super 15 win over the Rebels.
O'Connor appeared to be in extreme pain immediately after the incident and, although he attempted to play on, he was forced off the field of play with less than an hour gone of the Rebels' 30-21 defeat.
The Rebels are yet to confirm the extent of the damage to their summer signing but reports in Australia suggest the 21-year-old is a doubt for the internationals with Scotland (June 5) and Wales (June 9, 16 and 23).
Rebels head coach Damien Hill admitted O'Connor was having difficulty breathing and speculation has since surfaced that he may have lacerated his liver.
If that diagnosis is confirmed, O'Connor will be unable to take part in contact training for six weeks - almost the exact amount of time before the Wallabies take on Scotland in a one-off Test that opens their 2012 season.
O'Connor currently has 27 caps to his name having marked his debut with a hat-trick of tries against Italy in 2008.
Equally comfortable at wing, full back, fly-half or inside centre, O'Connor is expected to be one of the Wallaby dangermen when the Lions come calling in 2013.