It took a fine strike in the closing stages from Louis Thompson to break down the brave resistance of 10-man Shrewsbury.
The midfielder’s first goal for the club was enough to secure a third successive League One victory for Pompey.
That came after Aiden O’Brien had cancelled out Luke Leahy’s opener, with the hosts then seeing Josh Vela dismissed before the break for a late challenge on Ronan Curtis.
Cowley was pleased to see his side grab a valuable haul on the road, but felt the overall performance could have been better.
The Blues boss said: “It was an important result and when you win three games on the spin, you should be happy and smiling.
“We had a good start to the game and created a great chance that we couldn’t take, then conceded such a sloppy goal.
“That can knock you, but credit to the boys because we showed character and a positive response to get the equaliser.
"We’re pleased to win, even if we could have made it a lot easier for ourselves. We kept going and kept believing, though."
“Aiden’s scored again and the sending off soon followed. We knew what we wanted to do tactically, but some of our decision making was erratic.
“As a consequence, we couldn’t always find the rhythm and flow we were looking for in the second half.
“Steve Cotterill’s a very experience and pragmatic manager and with 10 men, they’re still a hard team to play against.
“But we need to control our emotions a bit better and there were a few players who gave the ball away too easily.
“We’re pleased to win, even if we could have made it a lot easier for ourselves. We kept going and kept believing, though.”
Cowley brought off defender Hayden Carter for Marcus Harness at the break, as he decided to change formations.
He explained: “Hayden was excellent and it was just a tactical decision because we didn’t need three defenders to build our play.
“It allowed us to have another attacking player on the pitch and that’s why we made the switch, but we could have executed that plan better.”