Yet he admitted the tired Blues failed to reach the high levels of the previous three victories since arriving as head coach.
Yet a leggy Pompey found it difficult to overcome the relegation-haunted Latics managed by Paul Cook’s former assistant boss Leam Richardson.
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Cowley conceded his side lacked intensity, particularly in the first half, and didn’t play well.
Nonetheless, considering the circumstances, he believes it represents their finest triumph yet.
Cowley told The News: ‘The first half we were half a yard or a yard off it, I didn’t think we were able to get the energy or the intensity in our pressing.
‘But it was our best win.
‘You are not going to play well for 46 games, so what you have to do – if you are going to be a successful team – is find a way of winning when you don’t play well.
‘In the first half we were short, the second half was better – and it was a brilliant goal from Andy Cannon.
‘We talk about getting control with midfield dominance in games and people think it starts with the ball, but actually it starts against the ball.
‘We were unable to get that intensity and, as a consequence, weren’t able to get as much possession as we would have liked.
‘I just felt we didn't quite do as well in the first half in the competitive moments as we could have done – and we certainly didn't make the first or second pass.
‘We couldn’t build from the back on this pitch, so couldn’t get the rhythm that way. Otherwise, to get the rhythm, you can spot and play, make sure your throw-ins are really good, making your switches and playing lines.
‘But we didn’t execute that as well as we would have liked. That’s the truth.’
Wigan signified a fourth win out of four matches since Cowley and brother Nicky replaced Kenny Jackett.
They had inherited a side dropping down the table and languishing 10th in League One.
Yet the Blues are presently fourth, five points clear of seventh-placed Charlton as the strive to cement a spot in the play-offs.
And Cannon wasn’t the only substitute that impressed Cowley during the latest win at Wigan.
He added: ‘Harvey White coming on as an 18-year-old, he made the first pass and the one that actually gave us a bit of control and composure.
‘Rasmus (Nicolaisen) when he came on made four or five headers in the box.
‘The finishers, as I like to call them, had a good impact and helped us win that game.’
A message from the Editor, Mark Waldron
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