League leaders Bayern were 2-0 up at half-time at the Allianz Arena on Saturday thanks to goals from Robert Lewandowski and Leon Goretzka, with Doll introducing Jonathas at the break.
The striker converted a penalty harshly awarded for a handball by Bayern defender Jerome Boateng but two bookings in quick succession then saw him dismissed.
Franck Ribery came off the bench to score a late third and secure victory for Bayern, moving them temporarily five points clear of closest rivals Dortmund.
"In the first 20 minutes, Hannover's defense were well marshalled but we had possession, although not too many goalscoring situations," said Kovac.
"After the 1-0 opener, we had a very good chance and we could have gone in 4-0 at half-time, then we'll have some rest.
"And out of the blue something happened, which was a penalty, but in my view it was not [a penalty], but we did our job."
Doll also disagreed with the decision to punish Boateng for inadvertently blocking a cross with his arm, the spot-kick given after a VAR check.
But it was Jonathas who drew the ire of the Hannover coach, with his side now needing to win their last two Bundesliga games to have any chance of securing survival.
The striker was booked for clashing with Bayern goalkeeper Sven Ulreich after scoring the penalty, then within four minutes he was shown a second yellow card for catching Joshua Kimmich in the face - a record turnaround for a player in the German top-flight.
"In the first 20, 25 minutes we did very well, then wave after wave rolls over you," said Doll. "We did not defend the goal for 1-0 well, because we have to be closer. But the boys did very well, [goalkeeper] Michael Esser did a great job.
"Out of the blue, that was a phantom penalty, as we've seen so often the last few weeks.
"The fact that we lose a player made me very, very angry, so you have to show a bit of tact as a referee."
Ribery's late goal enabled Kovac to bring on Arjen Robben for his first appearance since November and his 700th career game for club and country.
"These two have left their mark on this club in the last decade and they deserved it," Kovac said of the veteran wing duo.
"I would have liked to give them more minutes, but the game didn't allow it. It was amazing how the crowd reacted."