The second half continued as the first half, with Sale applying pressure through a physical forward unit and that pressure eventually paid off seeing Fowles score after a series of pick and drives.
Sale also added a couple of penalties to take a 13-6 lead into the last five minutes.
However, Munster showed great character when Darren Sweetnam scored a try under the posts, converted by Tom Kiersey in the 79th minute.
Unfortunately Munster could not hang to that lead, with Fowles kicking a penalty after Munster infringed at the breakdown.
Munster will complete their interprovincial warm up games next Friday, 31st August against Bruff first XV in Killballyowen at 7.30pm.
Munster XV: Darren Sweetman, Rob Jermyn, Harry McNulty, James McInerney, Alex Lynch, Tom Kiersey, Brian Haugh, Niall Horan, Will Foley, Brian Scott, Sean McCarthy, John Madigan, Jamie Kind, Jack O'Donoghue, John Fitzgerald (Capt.) Replacements Max Abbott, Cian O'Donnell, Dave Hartnett, Cronan Gleeson, Darren Ryan, Ben Nugent, Sean O'Leary, Darragh McNamara, Darragh Mulcahy, Rory Scannell, Dave O'Connell.
Sale Sharks XV: Tim Jeffers, Sam Bedlow, Mike Haley, Mark Jennings, Sam Broster, Sam James, Nathan Fowles, James Flynn, Tommy Taylor (Capt), 3.Ross Harrison, 4.Josh Beaumont, 5.Oli Parkinson, 6.Will Bordill, 7.James Doyle, 8.Danny Kennedy. Replacements: 16.George Hymes, 17.Jake Nickson, 18.Jonny Kenny, 19.Mike Finnemore, 20.Cameron Neild, 21.Billy Emerson, 22.James Mitchell, 23.Tom Deakin.
Munster U20 Interprovincial Fixtures
Munster v Connacht, Friday, 7th September, Musgrave Park, ko 7.30pm
Leinster v Munster, Friday, 14th September, Donnybrook, ko 7.30pm
Munster v Ulster, Friday, 21st September, Musgrave Park, ko 7.30pm
Ben Nugent leading his team down Heywood Road yesterday evening.