rbs6nations.com > Ireland
But Penney revealed it was a mere precaution with the aim of keeping the 34-year-old, who signed a new two-year deal with the club on Monday, fit for Ireland duty.
"He's fine. Just before half-time he got a bit of a knock on the shoulder, a bit of a stinger I think," Penney told the Irish Examiner.
"But he had a great 20 minute spell once he got over that little hiccup with the shoulder and we just took him off because he has a big month ahead.
"We didn't want to see him leaving us in anything other pristine condition so that he can do a great job for Ireland."
Munster's game against Edinburgh also saw two other Irish players pick up knocks, with Keith Earls similarly forced off in the second half with a knee problem while Peter O'Mahony struggled with an ongoing shin injury.
But Penney was not overly concerned about either in what was a boost to Ireland, who are looking to improve on last year's fifth-place finish in the RBS 6 Nations.
"He's (Keith) got a sore knee, it is probably short term and (likely) it will take a week or two," he added. "He'll get a scan Monday when he goes to international camp and we'll wait and see what the medics come up with.
"Peter got a bit of a knock, a bad knock on his shin last week and had a light week this week. Today he got a knock right on the same spot in the first minute but he played through. He'll be fine."