Jed Wallace restored parity in the 39th minute when he showed his composure by taking his time to send a measured rising 15 yard shot into the roof of the net with his right foot.
Hourihane profited when Yassin Moutaouakil failed to clear Rommy Boco's far post cross from the right and, six yards out, Argyle skipper Hourihane needed no second invitation to smash in his third goal of the season.
Whittingham said: "I think it was fair result overall and they probably started better than us but then we got back in the game at the right time.
"We were getting used to their three-at-the-back system and scored just before half time which gave us a boost.
"Then we came out and I thought for the first 20-25 minutes of the second half we were the better side and they came back into it before the end so probably, on reflection, it was fair.
"They changed it, they tried three at the back at Swindon in the week and we weren't sure if they were going to do it again because they hadn't done it all season.
"We talked about it a little bit but until the players were out there and seeing what they needed to do and then we just tidied up on it a bit more in the second half.
"Yassin Moutaouakil more than made up for his slip with his block at the end. I think that was a tremendous bit of defending from him and Jed is scoring a few this year, he's done well.
"I didn't make any subs because I didn't want to upset the balance and the lads had worked hard and did well against the shape."