Both players put in over 90 mins with Fowler coming off deep into injury time.
"They are still two games away from flying, but we saw good runs and forward thinking off them," said Jones.
"They didn't score, but on another day they could have got a hat-trick each.
"The important thing was that they got 90 minutes each and they feel OK after it - although I think they'll be taking the lift not the stairs at the hotel!"
Both players should be named in the squad to face Norwich this Saturday but it's not sure if either will be fit enough to start the game.
Jones gave credit to Leyton Orient and their keeper for keeping out around 25 efforts from City.
"Wherever we seemed to aim the shots they were just hitting some part of Nelson's body," said Jones.
"You get games like that and - full credit to Leyton Orient - they dug deep and battled.
"I just said to the lads that they had to keep going. They kept their concentration at the back and, after that, the goal was always going to come."