Emnes ended his recent drought with a goal in Saturday's win over Nottingham Forest - Boro's first victory in 2012 - and struck twice more to help sink Millwall 3-1 at The Den on Tuesday night.
"He's been through a bit of a barren spell and lost his confidence but now he's back," said Middlesbrough manager Mowbray.
"We are delighted he's back among the goals, we need him among the goals."
Emnes had already put a simple header over the crossbar before he got off the mark in the 14th minute, touching in a volley from Rhys Williams.
There was a touch of fortune about Emnes' first goal, but there was nothing lucky about his second in the 38th minute.
He collected Barry Robson's pass 35 yards out, skipped past some weak challenges on the edge of the area and thumped a superb low shot past David Forde.
But Millwall pulled one back with their first effort on target just before the break when Darius Henderson headed home.
The goal, their first at home in the league since Boxing Day, fired up the Lions and they improved vastly after the break.
But they could not find a way past Boro goalkeeper Jason Steele and the visitors wrapped up the points through substitute Curtis Main's first goal for the club four minutes before the end.
"Ultimately we are pleased with the points," said Mowbray.
"It's not easy to come here, you always know you are going to get a game but we showed our quality and should have punished Millwall more, we had some amazing chances.
"But we saw two sides of the Middlesbrough team, the quality we possess but also the fighting spirit and the ability to dig in."
Millwall remain three places and six points above the relegation zone and manager Kenny Jackett condemned their first-half display.
"We were very poor, we were physically not strong enough and we got bullied," he said.
"We have to look at ourselves, we weren't competitive enough or strong enough in the first half.
"We can't give ourselves a mountain to climb like that, but we did fight back with some spirit."
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