His fine cross created a first-half opener for Shane Long and then he put the game beyond Doncaster with a well-taken finish 13 minutes from time.
Billy Sharp, also on loan from the Blades, gave the home side hope with a penalty in the 80th minute after former Rovers' defender Matt Mills was dismissed for handball but Reading survived a late onslaught to claim back-to-back league wins for the first time this season.
Howard had wasted a decent chance by heading wide but he made amends six minutes before the break by creating the opener from the right flank.
Long was the beneficiary of Howard's inswinging cross, but Rovers manager Sean O'Driscoll was less than impressed by the quality of marking which left the Reading player free to head his second league goal in as many games. "I think we could have done better on both goals, to be honest," said O'Driscoll.
Long brought a good save from Neil Sullivan in the 70th minute before Howard made it 2-0 by rolling a low shot through a crowd of defenders.
O'Driscoll said: "Neil has played extremely well, but he might feel he could have done better with that one.
"But we came back into the game well. We never let our heads drop."
Doncaster were handed a lifeline in the 80th minute when Mills was dismissed for apparently handling Gareth Roberts's shot and Sharp sent Adam Federici the wrong way from the spot.
Substitute James Hayter nearly salvaged a draw in the 89th minute and O'Driscoll felt his side were worthy of more than a defeat.
"I think we are used to coming into press rooms having dominated, looking at positives," he said.
"We could have done better with the goals but I cannot fault anyone's effort.
"This league is so tight, you can walk off any game thinking you should have lost when you've won or won when you've lost.
"We try and maintain that players do the right things and as long as they do that we're happy.
"Sometimes results are in the lap of the gods, but overall I'm pleased with the way we played."
The result was not enough to lift Reading out of the bottom three while defeat left Doncaster in 17th spot.
Doncaster Rovers: Sullivan, Chambers, O'Connor, Martis (Hird 68), Roberts, Coppinger, Wilson (Hayter 73), Stock, Oster, Shiels (Guy 73), Sharp. Unused substitutes: Smith, Mutch, Heffernan, Dumbuya.
Reading: Federici, Griffin, Ingimarsson, Mills, Bertrand, McAnuff, Gunnarsson, Howard (Thorvaldsson 90), Karacan, Kebe (Church 60), Long, Church (Khizanishvili 82). Unused substitutes: Hamer, Rasiak, Pearce, Davies.
Referee: Keith Stroud (Hampshire).
This season the Yorkshire Post has an exciting new match-day service, called Match Centre. Here you will find minute-by-minute updates, stats and team formations. Plus reports from every game in England, from the Premier League down to the Blue Square Premier.
Simply select your game from the pull down menu, then click on the 'i' information button on the right of the fixture and it will give you access to everything you need to know about your team.
So if you can't make it to a game, head for the Match Centre and we will give you the best seat in the house. Click the link below.
For the latest team news, score and commentary from your team check out our new Match Centre