The 30-year-old was benched for the match, and struggled to make an impact even when introduced with 17 minutes left.
Giggs, speaking to ITV, was full of sympathy for his struggling team-mate.
"I see a player who’s going through a transitional period, I went through it when I was 29 or 30, where I was a winger and I couldn’t knock it around a defender and get it the other side," said the Welshman, who carried on playing at the highest level into his 40s.
"I feel a little bit sorry for him, towards last season and for England in the summer he was played in that deeper role, then he was told he’s playing as a No 9 or a No 10 [by Jose Mourinho].
"He’s probably a bit confused."
Giggs is certain that this is not the end of the story - but warned Rooney will have to work hard: "The only way he can get it back is on the training pitch," he added.
"I don’t see him playing in a specific position, he’s got the talent to play so many positions, and the experience."
PAPERS' VERDICT ON ROONEY
Sam Wallace, The Telegraph: "As Wayne Rooney came on to try to win this World Cup qualifier with 17 minutes left in Ljubljana he will have recognised a familiar kind of crisis... Without Rooney, the handbrake was supposed to have been released on Southgate’s young side, but they played with much of the usual fear and trepidation in the first half that is their 50-year inheritance...
"It was Rooney who was blamed in the past for slowing England down but even with him on the bench, the team were still stupendously ponderous... There were 17 minutes left when Rooney finally entered the game. He took up a position behind Sturridge and four minutes later made a run into the middle which only required a cutback from the Liverpool man that inevitably never came."
Matt Dickinson, The Times: "Oddly enough, all of England’s problems did not disappear with Wayne Rooney off the pitch. If anything, a whirlwind few months have shown that the more things change the more they stay the same among an anxious group of players. Sack Hodgson! Axe Big Sam! Dump Rooney! What next? Southgate out after four matches?...
"[When he came on] Rooney went close with one shot from the edge of the penalty box but departed with the same sense of frustration as the rest of his team. The omission of Rooney had made sense given that he has been in poor form. He wants the game played out in front of him these days, free to pick passes. With Slovenia so full of energy especially in the first half, it was easy to imagine that he would have been hassled amid a frenetic contest."
Matt Lawton, The Daily Mail: "[Rooney brought] some much-needed composure and leadership, not to mention a bit of inspiration... Here he was in the more advanced position he used to occupy with relish, in behind the striker. And he went close with one effort that whistled only inches wide. Indeed, had Daniel Sturridge not been so selfish Rooney almost certainly would have scored only four minutes after coming on. A simple square ball was all Rooney required. Sturridge, however, opted to go it alone."
OUR VIEW: Touching, misguided, but a healthy warning
There are major differences between the two players which make us wonder about the former Manchester United winger's judgement here. Giggs claims to have been 30 when he lost the ability to go past a man, but Rooney already hasn't done so for years. Forget Premier League defenders - he'd probably struggle to beat Kai in the back garden these days.
So while Giggs's backing for his former team-mate is kind and touching, it's hard to see Rooney playing through his 30s in anything like the manner the Welshman did.
One thing that Giggs said did strike a genuine chord, however: his exhortation to Rooney to get working on the training ground. Giggs was always among the hardest workers at United, while Rooney's reputation suggests that, frankly, he is not.
If he sorts himself out and throws everything into whipping himself into shape, his career might not be over. If he continues as he has done during 2016 so far, he'll continue to drift aimlessly in his career just as he does on the pitch.