Clark Robertson netted the opener with his first goal for the Blues against his former team, 10 minutes before the half-time whistle.
And Cowley’s much-changed side carried on their momentum as George Hirst burst through whipping a ball across the box to Marcus Harness before the former Rotherham striker turned provider to scorer, netting his ninth of the campaign.
The win reduces the gap to the play-offs to 10 points and the Pompey fans have been reacting to the victory on social media.
Here’s the Fratton faithful’s verdict on Twitter.
@pfcsam: Too late though. Should be getting results like that when it actually counts.
@ffslluke: Five games too late but great win.
@Hayden_PFC: Rotherham players struggling to sleep tonight after suffering nightmares of Mr Hirst. Shown them real levels today. Up the Blues.
@al3xmacdonald_: If we beat Cheltenham we might actually of had a chance!
@HazzaTWood96: A 3-0 home win against Rotherham, who saw that coming after the Cheltenham result.
Congrats to Captain Robertson on his first Pompey goal and to Harness and Hirst for adding to their tallies as well.
One of the best results this season, PUP.
@pfcdave1898: Well done lads, fantastic response from Saturday.
@MammothEU: Getting beaten by Cheltenham and smacking Rotherham is the most peak Pompey thing.
@JamiePFC: Why do we suddenly perform now? Needed it after last weeks performance though.
@HarvMarksy: From that performance alone one of the worst I’ve seen this season.
George Hirst absolutely unplayable today, clearly had a point to prove.
Shame it means nothing but enjoyable one this evening. Back on Friday.
@PFCperspectives: We’re a funny old club aren’t we?
What a brilliant performance.