The former Ireland Under-20s youngster has caught the eye with a series of impressive performances for Munster but he was not at his best the previous week against the Scarlets.
As a result, Penney rang the changes - making 14 in total - but stuck by Hanrahan, and it paid dividends as Munster stretched their lead at the top of the RaboDirect PRO12 table.
"He didn't have the best of games last week [against Scarlets], but he is an assiduous, conscientious young man who is trying hard," Penney told the Irish Examiner.
"He has good people around him, [coaches] Simon Mannix and Ian Costello are working hard with him and it is bearing fruit, he is a talented kid who's making huge progress.
"JJ was terrific, we all know he's a prospect and where we want him to get to, he is getting better and better.
"I am pretty pleased [with the result] given the conditions and the competitive nature of Connacht-Munster games historically. We dominated for large parts and deserved our victory. They came to disrupt us and play and they deserved their [losing bonus point] result at the end."
Dan Parks kicked Connacht into an early 6-3 lead before Hanrahan dotted down and converted, adding another penalty before the break for a 13-6 half-time lead.
Three further penalties from Hanrahan made the game safe but Connacht secured a losing bonus point thanks to David Heffernan's last-minute try, converted by Parks.
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