Winnall and Batth were making their senior debuts for the club and Hemmings his first start, in a Wolves side featuring 10 adjustments from the one which drew 1-1 at Everton on Saturday.
The trio, all 19, each played their part in the Carling Cup tie, with centre-back Batth given a testing time by a spirited Shrimpers attack and Hemmings and Winnall combining well up front.
The latter earned the first-half penalty which Nenad Milijas converted to put the Premier League outfit in front.
Southend deservedly forced extra-time after their captain Craig Easton headed past Wayne Hennessey in the 80th minute, but Wolves skipper Richard Stearman had the final say, bundling home Ronald Zubar's cross in stoppage time at the end of the second additional period to send Wanderers through.
It was a victory McCarthy admitted his team did not deserve, but the manager was more than satisfied with the performances of the three teenagers.
"The three young lads were great, I was delighted with them," McCarthy said.
"It is always a gamble. If I had just played those two up front and Danny Batth with eight of the others that had played on Saturday, you might have seen even more from them.
"They didn't have that solid base, and they have come into a team that has completely changed, albeit they have trained together for the last week or 10 days.
"I was pleased with them - I thought Sam Winnall was great getting the penalty and Ashley Hemmings worked hard and did his little bits.
"Big Danny Batth had a tough game and had to fight for every single ball, so it was positive on the night - the result, and the performance of the three young lads."
Winnall suffered a cruciate knee ligament injury last year and was keen to thank the club's head of medical department Steve Kemp, physiotherapist Alan Peacham and masseur Mark James for helping him recover to make his bow for the first-team.
"I haven't had chance to say it before but I think I owe everything to the medical staff here," Winnall told the club's official website.
"Kempy, Peachey and Mark James have all been tremendous with me.
"They've made my injury, which is not a nice injury to have, as easy as possible for me to come back.
"So I'm forever grateful to all the medical staff for how they helped me through.
"It was a tough time, no doubt about it, and it made me mentally stronger because I had to be so driven and determined to come through it.
"But the medical staff were brilliant and helped me so much with the injury and then the rehab, so I'm really thankful to them."