The Celtic boss went in to the game without Glenn Loovens, Emilio Izaguirre and Beram Kayal who were all out through injury.
And he watched in dismay in the 63rd minute as Hooper immediately signalled to the bench his distress following a challenge from United defender Paul Dixon, just after the Celtic striker had got a shot away.
Lennon confirmed Borussia Monchengladbach striker Mohammadou Idrissou would be coming to Lennoxtown on Monday for a few days training, saying: "We have checked him out before and it is worth a look for him."
However, with a view to Thursday night's Europa League first-leg clash with Swiss side Sion at Parkhead, the Irishman is hoping a scan on former Scunthorpe striker Hooper will bring good news.
"This injury seems to be in vogue at the minute," said Lennon.
"He rolled his ankle with the impact from the shot and the challenge from Paul Dixon, although there was nothing malicious in it.
"We will have Gary scanned on Monday and with a bit of luck it will not be as bad as Kayal's.
"He could be (okay for Thursday) but I wouldn't like to call it.
"Kayal felt a lot better but it could be a stretch to make Thursday night but you never know, fingers crossed.
"It's not been great with some of the players who have picked up knocks but you could see the strength of the squad and the substitutes who came on were brilliant and made a huge impact as Dundee United were tiring."
Hooper had headed Celtic back in to the lead just before the break after Johnny Russell had cancelled out Anthony Stokes' early opener.
Further goals from Ki Sung-yueng, Joe Ledley and substitute James Forrest put a gloss on the scoreline.
However, it was much-maligned keeper Lukasz Zaluska who was named sponsors' man-of-the-match - and Lennon denied that any keeper he might sign is guaranteed to take the Pole's position.
"That's not necessarily true. When we brought Lukasz in last season he did very well," said the former Celtic skipper.
"He is playing well and he had no chance with the goal.
"But I need to bring a keeper in because if Lukasz gets injured then we only have Dominic Cervi and nobody else.
"So it is important that I bring another keeper regardless of Lukasz's form
- and he played very well today.
"We know he is a good goalkeeper."
Lennon admitted he enjoyed the afternoon.
"It was a fantastic result," he said. "Five different scorers, different goals as well and we could have had more.
"We were open at the back at times but to beat Dundee United 5-1, we couldn't ask any more from them."
United manager Peter Houston, though, claimed his side had only themselves to blame for four of Celtic's goals.
"It was a sore one in the way we defended," he said.
"I felt that they got four of their goals quite cheaply and the only one they worked well was the goal by Ki.
"The goals that we lost were very disappointing.
"The first one was a bread and butter save, our keeper fumbles it and they get a corner and they score from it.
"If we do our jobs properly we don't lose that type of goal.
"We get to 1-1 and then we lose another goal from a corner kick.
"The most disappointing things was the fourth and fifth goals.
"Ledley had more desire to get there than our defender and then at their fifth goal our heads were down and we were tired."