The Pirates have lost just once in eight games since Ward took charge before Christmas.
This victory avenged a 2-0 win by Oxford at the Memorial Stadium at the start of the season and pushed Rovers further clear of relegation danger.
Lee Brown's penalty 10 minutes into the second half, and a second goal deep into stoppage time by substitute Eliot Richards did the trick.
Ward said: "It was an exceptionally hard game for us, our third game in the week, and on a pitch that was massively heavy.
"We had to battle our way through this one. Oxford's manager saw us play on Tuesday and set his team up to make it very hard for us.
"But we did ever so well. We are keeping our nerve under pressure, collectively and individually, and it just shows what winning matches can do for your confidence.
"We've defended stoutly, as we've had to, and the second goal was quick thinking and some very good play.
"It's happening nicely for us at the moment and we're enjoying it.
"But after these three games in a week, the boys badly need a break and a breather now, and we'll allow that to happen."