Jones' side took the lead shortly after the break, O'Brien and Bleyendaal trading penalties, before the young Welsh pivot put the hosts ahead.
But Cian Bohane dotted down what proved to be the winning try on 55 minutes as Munster rebounded from last weekend's loss to the still unbeaten Cardiff Blues.
And Jones couldn't help but think that an opportunity had passed his side by as they engineered a driving maul close to the Munster try-line in the final minutes, only for the opportunity to go begging.
"It's the same hard lines story for us," he said. "We were one good driving maul away from being in a very good place but that's the fine margins of rugby at this level.
"These are the types of games we have to turn from defeats into victories if we want to progress."
Newport Gwent Dragons sit seventh in the Guinness PRO12 table, one place and four points behind Munster as Rassie Erasmus's side racked up their second win of the campaign.
And it might not have been pretty but South African Erasmus admitted he was simply happy to pick up another hard-fought win.
"We had to work very hard but I thought we fully deserved the win," Erasmus said.
"It wasn't pretty, but again the side showed guts."
Guinness PRO12 Final 2017 Ticket Information: Fans can save up to 20% on selected tickets, and prices start at just €30 adults and €5 child, and be booked via www.ticketmaster.ie. For further information visit http://www.pro12rugby.com/final
Guinness PRO12 Dragons News
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