The 26-year-old Dutch wide man, who signed a four-year deal from Ajax in midweek for a reported fee of £3million, was replaced by Tony Watt near the end of the first half of his Hoops debut against Ross County at Parkhead after picking up an ankle knock.
Lennon turned his thoughts to Sweden where his side will try to defend a 1-0 first leg lead and he is worried he may have to do it without Boerrigter.
The Parkhead boss said: "You can see what Derk brings to the team, that pace and balance on the left. He was coming in off the line well when James Forrest was down the right-hand side.
"He looked a real threat in the first half but we have a bit of a sweat on for Wednesday night to see how he is. He jarred his ankle. It was a total accident, he clipped Mihael Kovacevic's Achilles and it has twisted. So we will have to see how he is."
Georgios Samaras (toe) and Kelvin Wilson (shin splints) missed the game, but Lennon said: "We are hoping they will be okay. Georgios is still very tender. Kelvin gets shin splints this time of year, so he should be okay for Wednesday."
The former Celtic skipper praised Stokes who has replaced Gary Hooper as the focal point of the Parkhead attack since the Englishman left for Norwich.
Lennon said: "Anthony is a goalscorer. His record here is excellent. He may not get the volume of goals that Gary Hooper got but if you look at his record, I think it is one in two games in Scottish football, so he is one I wouldn't want to go.
"I just want him to play the way he has in the last three years, he has weighed in with a lot of important goals and the volume of assists is very good."
The Northern Irishman praised his players' performance despite the chances missed before Stokes got an 87th minute winner.
He said: "Even if we had drawn I would still have been pleased with the overall performance. I thought we were terrific today and deserved to win the game. There was a real zest and pace about us, our movement and passing was good and on another day we could have racked up a good score.
"We worked the goalkeeper really well, we hit the post and had umpteen balls flash across the box but the build-up play was very good, something we haven't had for a wee while."