Much of the attention at Easter Road surrounded the 23-year-old, who has been the subject of two failed bids by Rangers – the highest of £225,000 – but he was named among the substitutes and came on in the second half to cheers from both sets of fans when the home side were chasing the game.
Sam Stanton gave Hibs the lead in the 13th minute but their Championship rivals responded with goals from right-back James Tavernier, a double from striker Martyn Waghorn, Andy Halliday and a late brace from substitute Kenny Miller, rendering Jason Cummings’ earlier spot-kick a consolation.
Afterwards, Stubbs reiterated Hibs’ stance with regards to Allan before revealing why their star player had not started.
He said “I will answer with three words. Not for sale.
“I am not going to keep answering questions on it. You have to respect a club’s stance when you say a player is not for sale.
“I spoke to him before the game. I don’t think it would have been right for me to have put Scott in the game today with what has been going on, the circus of the last few days.
“He is a professional footballer, he is a human being, it would have affected him.
“The most important thing was the team and the club. I said to Scott that I was doing it for him and the club.”
When questioned on whether Allan had asked to leave Hibs, Stubbs said: “It’s irrelevant. He’s got one year on his contract.
“He can go for nothing at the end of the season. He can sign a pre-contract in January. He will have very good options if he sticks it out.”
Following victory in his first competitive match as Gers boss, Mark Warburton fended off questions about Allan, saying: “He is not my player. If I was Alan Stubbs I would be irate.
“My job is to talk about Rangers players and as far as I know Scott Allan is not a Rangers player. He is a Hibs player and it is disrespectful for me to even comment on that.”
The former Brentford manager was happy with the way his players responded following a “four out of 10” first-half display.
“I am happy with the result but not happy with the first-half performance,” he said. “We could have been two or three down.
“The players are an honest group and the first half was below the required level but I got a good response after half-time and a pleasing result.”
On the game, Stubbs said: “Two lapses in concentration turned the game on its head from us being on top to the scoreline at half-time being harsh. 6-2 was a disappointing result but we contributed to a lot of the goals today.”
Stubbs also revealed an interest in John McGinn, who is out of contract at St Mirren.
He said: “We will see over the next few days. We have spoken to John McGinn and that’s all I can say.”