Louis van Gaal's side suffered their seventh Premier League defeat of the season on Saturday, going down 2-1 to Sunderland at the Stadium of Light.
The result leaves the Red Devils in fifth place in the table on 41 points, six points off Manchester City in the final Champions League spot, having played a game more.
Rooney admits Champions League football for next season now looks unlikely and has urged his side to pick themselves up ahead of their midweek Europa League clash against FC Midtjylland.
"It will be difficult to qualify for the Champions League through the top four now," he told BT Sport.
"We didn’t create enough chances, weren't aggressive enough and didn’t defend set pieces and it’s cost us. It’s a disappointing result.
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"I think we didn’t play well today we know that we didn’t win enough second balls. It’s cost us and it’s not good enough. So it’s a sad day for us, disappointing in terms of losing three points. We have to some how move on
"It’s [the Europa League] a competition we didn’t want to be in but we’re in it now and want to win it. We have to try and start again on Thursday."