O'Connell, who only returned to action from a long-term groin injury in March, left the field in considerable pain with an ankle injury and the former Heineken Cup Champions will have to wait for further medical examinations this week before discovering the full extent of the problem.
Leinster head coach Joe Schmidt expressed his hope that the injury was not as bad as first feared.
"It was disappointing for Munster to lose Paul and he is not the kind of guy to leave the field unless he is in considerable pain and I just hope the injury is not as bad as it looked as when he went off it looked pretty bad. Hopefully he will be fit again next weekend to help Munster in their Amlin conquest," he said.
In a typically frantic encounter, the rugby was of the highest quality in West of Ireland and both sides will take confidence from their performances ahead of their last eight matches in the Heineken and Amlin Challenge Cups next weekend.
Irish fly-halves O'Gara and Jonathan Sexton exchanged two penalties apiece in the opening fifteen minutes before Sexton kicked his side into a 9 v 6 lead.
Moments later Isa Nacewa broke clear down the right and his kick through was collected by Shane Horgan who crashed over in the corner for the game's opening try.
O'Gara then kicked a further penalty for the hosts before Sexton converted two of his own to take Leinster into the break deservedly 20 v 9 ahead.
The second period was all Munster and Paul Warwick, a blood replacement for O'Gara, narrowed the deficit by a further three points with penalty before O'Gara returned to the field and kicked six more points to take the scores to within two.
As the game entered the third quarter, Leinster lost Brian O'Driscoll to the sin-bin and O'Gara kicked his fifth penalty, this time from 50 metres to regain the lead for Munster.
Sexton kicked Leinster back in front and looked to have won the game for the visitors before O'Gara's final kick at the death.