Johnson cancelled out Kevin Doyle's opener midway through the first half but was forced off shortly after with a sore knee.
He will have a scan Wednesday morning to determine the extent of the injury, but he is expected to be out for at least two weeks.
Dowie believes Johnson has become a target in the Championship and was only denied a penalty because of his reputation for diving.
Reading shaded a cracking first half which ended 1-1 but could have been much more.
Doyle, a £75,000 bargain buy from Cork City, put Royals ahead with a stunning 26th minute strike for his third in three games.
But the home side's celebrations were cut short by Johnson just three minutes later when the England man held off Ibrahim Sonko before firing past USA keeper Marcus Hahnemann for his sixth of the season.
However, that was Johnson's last contribution after he pulled up holding his knee after 37 minutes.
Palace, though, regrouped and stunned Royals by taking the lead just two minutes into the second half through Clinton Morrison's volley.
The visitors should have made it 3-1 soon after, but Hahneman expertly saved at Michael Hughes' feet.
That flaring miss soon came back to haunt Palace when Leroy Lita equalised with a spectacular overhead kick in the 68th minute from Glen Little's cross.
But Lita nearly blew Royals' hopes of victory when his 75th minute penalty was saved by Palace keeper Gabor Kiraly after Doyle had been tripped.
However, referee Brian Curson ordered a re-take and Little saw that one superbly saved again by the Hungarian skipper.
Even so, Dowie was so incensed with the officiating he was ordered from the dugout for berating the fourth official.
Meanwhile, Royals pressed for the winner which eventually came two minutes from time when Sonko headed home from Little's cross to extend Reading's unbeaten run to eight games.
The defeat also ended Palace's three-match winning run in the league and Dowie must now find a replacement striker for Saturday's daunting trip to Cardiff.
Royals boss Steve Coppell said: "It was a great game and we did a lot of good things which will stand us in good stead for the rest of the season.
"Palace are a top outfit but we had a bit of good fortune out of Andy Johnson's misfortune.
"He is a real cutting edge for them but it shouldn't detract from our performance."