The Manchester United manager chose to travel to Spain to watch forthcoming Champions League opponents Valencia, leaving Phelan in charge for the third-round clash at Glanford Park, which United won 5-2.
The reigning champions have in the past been criticised for fielding weakened teams in the competition but, even though they made 11 changes from the 3-2 win over Liverpool, the most notable absence from Wednesday's teamsheet was on the bench.
Ferguson has only missed two previous competitive games in his 24 years at the Old Trafford helm, but Phelan defended the Scot's decision and insisted United have already proved their commitment to the cup.
He said: "We put a big value on the Carling Cup. We've never set out to demean the Carling Cup. We're holders, we've done that two years in a row and you can see from the players' attitude that we want to keep hold of it."
Ferguson's absence also showed how important he deems next week's Valencia match to be after United's failure to beat Rangers in their opening Champions League fixture at Old Trafford.
Phelan continued: "It's important after the Rangers games that we prepare properly and get a good view of Valencia, who've started their season very well.
"He chose to go and watch the Valencia game. We need to go there knowing what we're up against. He's the manager and he had to make a decision."
On a night when Chelsea, Liverpool and Manchester City all lost, Phelan was happy just to make progress, and it looked like Glanford Park could witness the biggest upset of the lot when Scunthorpe came flying out of the traps.
They had already had a number of chances when Josh Wright crashed a shot into the top corner after 19 minutes, sending the record crowd of 9,077 into raptures.
But it took only four minutes for Darron Gibson to level with a sublime lob and Chris Smalling gave the visitors an undeserved lead at the break.
Within nine minutes of the start of the second half, the result was settled, with Michael Owen scoring a breakaway goal and Park Ji-sung clinically tucking away the fourth.
Owen tapped in his second and United's fifth but the excellent Martyn Woolford at least ensured Scunthorpe had the last say with an injury-time strike.
Phelan said: "I thought Scunthorpe played their part in a very, very good game. They created plenty of opportunities, even when we managed to get it to 5-1 I think we'd had about six chances.
"Overall it's a great scoreline from our point of view because it was a new team out there put together in a couple of days, and Scunthorpe should take a lot of pride and credit from the game."
For Scunthorpe caretaker manager Ian Baraclough there were mixed feelings as his side were punished for their adventurous spirit.
The 39-year-old former Iron defender was taking charge of his third game following the departure of Nigel Adkins to Southampton and he revealed he will sit down with chairman Steve Wharton on Thursday, when a decision will be made on his future.
Baraclough said: "It could have been so different but it wasn't to be. The lads won't be too down about it, I won't let them be.
"They finished clinically. I've just been told we had 25 efforts on goal, we've made their keeper work 14 or 15 times. I couldn't fault the lads, we just kept going forwards, but we left ourselves open a bit.
"We learned a harsh lesson tonight but if you do that to any team, not just Manchester United, they'll punish you. We got caught up in the atmosphere a bit and the excitement of taking the lead."