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But Ronan O'Gara's 73rd-minute penalty made sure Munster came away from France just a point behind group leaders Sale Sharks at the halfway point of the pool stage.
O'Connell said: "Clermont is a difficult place to come and sometimes the bonus point is the most important thing in a group as tight at this, especially after Sale got a bonus-point win this weekend to get them right back in it.
"But we're still disappointed to lose because things were going well for us in the first half.
"We had a poor first 20 minutes before Marcus scored his try but we showed great resilience to get in position to earn the bonus point and at the end we were pushing hard for the win."
Marcus Horan barged over to hand Munster a 13-6 lead on 25 minutes after O'Gara and Brock James traded kicks, but the champions failed to build on that early blow after conceding a series of penalties.
O'Connell said: "We scored a great try but we made the mistake of allowing them to build momentum.
“There were a few mauls that we didn't pull down and that allowed them to open space out wide.
"We gave away too many penalties in the wrong areas and they made us pay on the scoreboard. We will have to tighten up on that next week.
"We've got two games left at home but we're still only half-way through the pool and plenty can happen."
Clermont-Auvergne had to win to stay in contention after losing their opening tie to Sale and outside-half James responded, scoring all his team's points, including six penalties and a second-half try in a man-of-the-match display.
James said: "We have had an inconsistent season so to put a good foot forward we knew we had to get a result against Munster.
“We're pleased to get it, but now we have to back it up when we go to Munster next week and Sale after that.
"Munster did a great job of slowing our ball when we had space out wide but I thought we controlled the game and the more field position we held, the more the points came.
"But we know the size of the challenge next week. Munster are the top side in Europe so we will have to be at our very best to get anything there."