The 2009 British & Irish Lions skipper missed much of the first-half of the season with a nagging groin injury and had recently been getting back to his very best form in time to lead Munster in their quest to win two major titles this season.
"After retring injured in the 46th minute of last night's Magners League game against Leinster at Thomond Park a subsequent X-Ray at Limerick Regional Hospital established that Paul O'Connell hadn't suffered a fracture to his left ankle," said a Munster statement.
"The Munster captain will travel to Dublin early this week for specialist medical examination to determine the full extent of the injury."
A Ronan O'Gara penalty 10 seconds from time clinched victory for Munster after a stunning second half come-back by the home side in front of 26,000 supporters in Limerick.
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 9-6 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 20-9 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.