Redcar-born Jordan Jones, 18, became the 41st debutant since the Academy system began when he replaced Luke Williams on the hour mark of the 4-1 FA Cup with Budweiser win over Hastings United.
And Bryn Morris, from Hartlepool, became the 42nd and the third youngest player to have played in a first team match for the club, at the age of 16 years and 254 days, when he came on for Merouane Zemmama with eight minutes remaining.
"Hopefully their appearances give them some encouragement to keep working hard," said Mowbray.
"Jordan has fabulous talent and likes to move the ball and drift past people. It's okay doing it at under-18 level but it's very different in the first team.
"He's a player who excites us all and in years to come the fans are going to enjoy seeing him travel with the ball and doing his stepovers."It will probably be a year or two down the line before he surfaces again, but we've given him a taste of it.
"Bryn is a young boy who there's been a little bit written about. He's captain of England Under-17s and is another Boro Academy player with real potential.
"He's a footballer I like. He plays economical football and his control and passing are very tight.
"He's also very athletic and can get around the pitch all day long, yet he's only just left school and he's got to work extremely hard.
"We shouldn't have too high hopes too soon but he's got a bright future in front of him. He's also potentially a year or two away from threatening our team.
"There are other boys who could easily have got in and some from the Under-21s might feel it should have been them.
"But we were a bit short of holding, passing midfielders and Matty Dolan has gone on loan to Yeovil, which is better than sitting on the bench for us.
"Jordan has something we didn't have. They got their opportunity because of injuries and we gave them a chance."
Meanwhile, Mowbray confirmed that Andy Halliday, pictured above with Seb Hines, has had an operation on a broken nose sustained at Derby and aggravated against Hastings, but he is not expected to miss any games.
"By the weekend I'm sure he'll be fine and if not we hope George Friend won't be too far away," Mowbray said.
Mowbray is keen to tie the former Livingston man down to a new contact after he impressed while deputising for the injured Friend in the left-back role.
"We would like Andy to stay," the manager said. "We would like him to sign a new deal and get on trying to progress his career.
"He's doing very well but he's still got a lot to learn and hopefully he thinks Middlesbrough is the right place for him to do that."