The Dragons led 9-7 at the interval through superior territory and possession, only to concede four tries after the restart to fall to a 38-12 defeat against Anthony Foley's side.
The result consigned Jones' men to their third defeat in four home GUINNESS PRO12 games this season, with only a solitary victory over Benetton Treviso in round four.
And although Jones insists there was plenty to cheer about in the Dragons' first-half display, he acknowledges that his players found themselves overwhelmed in the second period.
"We had been making progress since the Edinburgh game and had really picked up our performances," Jones told the South Wales Argus.
"I said to (head coach) Kingsley Jones at half-time, 'what we have got out of this group is just superb' because we had hurried and harassed Munster.
"We stopped them getting their game going but with so much possession and territory we should have been 19-7 up, not 9-7.
"But second half we got outdone - they put the pressure on us, we couldn't get out of our 22 and as they scored more points our heads dropped."
Click here to view the best images from Munster's victory over the Dragons.
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