Utility back Jones had only recently returned from a career-threatening neck injury that ruled him out of the majority of last season and now the 23-year-old finds himself sidelined with cruciate ligament damage.
Fogarty will be missing until after Christmas after picking up a shoulder injury that required immediate surgery.
Fogarty's absence adds to head coach Tony McGahan's woes in the front-row, with Ireland hooker Jerry Flannery yet to make an appearance this season.
Dowling was forced from the field after four minutes with a hip injury and the winger must now wait for further results before the full extent of the lay-off is known.
Munsterare unbeaten so far this season, sitting one place above fellow Irish outfit Ulster in the Magners League table.
McGahan's men travel to Scotland to face Glasgow Warriors on Friday, September 24, as they look to make it four wins from four.
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