The Millwall boss felt Charles Breakpspear’s dismissal of the Blues right-back was ‘really harsh’ as his side advanced to the second round with a 2-1 win at The Den.
Johnson was given his marching orders shortly after the restart for a challenge with Lions striker Tom Bradshaw.
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Rowett felt a challenge in the build-up to the incident was worse than anything Johnson did, and he was unlucky to walk.
He said: ‘In my opinion, the sending off changed the game.
‘It was never a sending off, it was really harsh.
‘I thought the first challenge was poor but the second challenge, if I’m honest, never truly warranted a red card.
‘I felt it made it difficult for us because they then sat in.’
Rowett, who was raised on the Isle of Wight and watched Pompey as a youngster, had praise for Danny Cowley’s side as they emerged with credit from the first-round clash.
Reeco Hackett-Fairchild rifled Pompey in front before two goals in six minutes for the home side turned the game on its head.
Rowett added: ‘I felt we looked a little big edgy early on and Portsmouth started well, they’re a good side.
‘They’ve got good strengths but we settled down, played the ball side to side and were probably the better side.
‘The two goals were good examples of us doing that and they were good moves, and, in my opinion we were fairly comfortable in the end in the first half.’
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