Johnson feels Bristol City pushed their Premier League opponents to their limits in the 2-1 defeat at home.
The defeat saw the club's best EFL Cup run for 27 seasons come to an end at Ashton Gate but Johnson said after the game he was pleased with their efforts.
Speaking to Bristol City Player, he said: "I was very proud, particularly of our young players because I thought they were outstanding tonight.
"In the last half hour we played som exceptional football - neat, tidy, intricate play with one-twos and attempts on goals.
"We've put together a group of generally under-24s with a little bit of experience and it's important that we play them and give them the opportunity to shine.
"I feel disappointed that we've lost the game but it's a fantastic marker for us to move forward."
Hull bested their Championship opponents with two goals from two set pieces.
Both balls were headed in from corners by Harry Maguire and Michael Dawson either side of half-time.
But Bristol City were far from out of their depth against a more experienced side, holding 49 per cent of possession and consistently pressuring the Hull goal with 20 goal attempts and six blocked shots.
Johnson added: "In my opinion, in general play, we were the better side. That bodes so well for the club and for the future."
Bristol City have started their season off positively, currently sitting in sixth place in the league with 23 points to their name.
They have bagged encouraging wins over the likes of Leeds United and Aston Villa and look like strong promotion contenders should their form continue.