Dowling had to be taken off in the fourth minute of the league clash with the Ospreys, with Jones replaced by Danny Barnes in the closing minutes of the game.
Both players will seek further specialist advice but initial indications are that they face lengthy period of rehabilitation.
It is particularly cruel luck for Jones who had only just made his comeback from a serious neck injury which he suffered last December against Connacht.
The 23-year-old had started Munster's first three games in this season's Magners League, scoring his first try for the province against Aironi Rugby.
Meanwhile, Denis Fogarty, who was replaced after 29 minutes on Saturday night, underwent a shoulder operation in a Dublin clinic this morning (Monday).
Fogarty will be out of action until after Christmas, joining the likes of fellow hooker Jerry Flannery and team captain Paul O'Connell on Munster's long term injury list.
However, there was encouraging news from the 'A' Interprovincial last Friday night. The Munster 'A' side's 30-3 victory over Ulster Ravens saw the return to action of Lfeimi Mafi, who scored a try, and Denis Hurley, Sean Scanlon and Academy hooker Sean Henry were among the standout performers.