It was a poor display by the City team as they failed to create any serious chances against a solid and determined Plymouth side.
Leroy Lita and Simon Clist forced good saves from Argyle keeper Kenny Schofield early on but City failed to capitalise on the bright start.
The game was decided by a 55th minute penalty awarded for an off-the-ball incident. Hasney Aljofree sent Stowell the wrong way from the spot-kick. Even after Plymouth’s Ben Steward was sent off with five minutes left City never threatened to get back into the game.
Coach Shaun Taylor was bitterly disappointed with the performance.
"We have put in some good performances this season, but I told the players afterwards that they have to achieve greater consistency.
"They have a great stage at Ashton Gate and should be giving everything to show they can make the next step into the first team squad.
"Even if they are not playing well you want to see signs of that attitude."
City Reserves: Stowell; Simpson, Aubrey, Woodman, Harley; Lambu (Anyinsah), Clist, Hulbert, Hawkins (McGuire), M.Brown, Lita.
Plymouth Argyle Reserves: Schofield: Connolly, Villis, Aljofree, Hodges; Phillips, O’Sullivan, Steward, Beresford; Lowndes, Yetton.