Flynn and Jones were placed in caretaker charge after boss Dean Saunders left for Championship outfit Wolves on Monday with Stevenage striking first in the 66th minute through James Dunne.
Doncaster fought back and Iain Hume equalised 13 minutes later before Jones rose highest to meet a David Cotterill left-wing corner four minutes into stoppage time.
"Let's enjoy the moment and see what develops this coming week," said Flynn. "It's good to be back in management, good to be working with good players.
"I've not heard anything from (chairman) John Ryan as we speak, I'm just looking forward to the Leyton Orient game which is next. For Rob it has been an ideal week, an absolutely ideal week. We've worked well together, we've got on really well and we've made decisions together.
"Thankfully all the decisions we made were right. They're a good bunch of players. We've got a good blend. We've got really quality defenders, people who can create something out of nothing.
"We've got midfield players who know their job, both with the ball and without it and we've got match winners and that's not a bad combination to have all of them.
"The performance from start to finish was very good and the finish was exceptional. To end the game in such a manner is a credit to the players, their fitness levels are fantastic."
Meanwhile, Stevenage boss Gary Smith could not get to grips with how his team failed to pick up something from the game at Broadhall Way.
He said: "From our point view, the winner is a really poor goal to concede so late in the game. Through all of our work, endeavour and quality in the game, to come away with nothing again is heartbreaking."
- Sports & Recreation
- David Cotterill