Former Cardiff player Gestede netted for the second league game on the spin when Jordan Rhodes stood up a great cross on the stroke of half-time for his fellow frontman to head home from close range.
Blackburn have lost just once in their last eight matches across all competitions and their seventh clean sheet at home in the league this season leaves Bowyer's side two points off a place in the top six.
The manager was quick to praise Gestede, saying: "He's going to get better and better, the big man.
"He's settled in very well, very quickly and had a massive effect in the last three games that's for sure. But he's going to get better as he gets fitter and stronger and be a real handful."
Bowyer also lavished praise on goalkeeper Paul Robinson.
The former England international made his first league start in 13 months after injury and illness and guaranteed the points in stoppage time with two magnificent saves, brilliantly tipping over an Alex Peterson header and then palming away a volley from Richie Wellens.
Bowyer said: "He's not had a great deal to do, especially in the first half, but it just shows you how important his experience is to us. He's not been in the game much and then he has to produce something like that. Brilliant."
The Blackburn manager described it as a "massive win" and was pleased that his defence could see the game out after the blistering first-half performance level died down in the second half.
"It was a massive win, a very important win after the Manchester City game because expectations go through the roof, so full credit to the players because they were very professional today and stayed focus on the job in hand against a very difficult Doncaster team," Bowyer said.
"We were excellent in the first half, played some great stuff and should have been a couple of goals up, scored a fantastic goal.
"The desire Rudy showed was unbelievable and then we've had to see the other side of the game we've developed over the course of the season: the doggedness, character and spirit and an outstanding save from Paul Robinson. Overall it was a huge win for us."
Rovers drew against Premier League title contenders City in the FA Cup third round last Saturday and have a replay to look forward to on Wednesday.
"The emotional side of last week's performance was something we were concerned about going into today," Bowyer said, "but I can't praise the players enough. They've been fantastic."
Doncaster boss Paul Dickov took heart from his team's spirited second-half performance.
Doncaster have never won at Ewood Park, and have now taken two points from their last nine away games, but Dickov felt the margins between getting something out of the trip and losing were small.
He said: "I thought Blackburn started really well, pressed us and put us on the back foot. We weathered the storm and there was nothing in the game.
"Us giving the ball away sloppily just before half-time and a lapse of concentration to let Rhodes get in has ended up being the difference.
"I thought some of the stuff in the second half was excellent and we were unlucky yet again.
"Paul Robinson showed why he's an England international with the two saves at the end because the first one was special. I've just seen it again and it was top class.
"The difference today is we've made one mistake and been punished, and Paul Robinson.
"Once the squad looks a bit stronger and we continue with the performance of the second half, it might be daft, stupid, naive or all three but I know we'll be okay this year."