Celtic struggled to create a clear opening before right winger Kris Commons dispossessed Richard Foster and set up Stokes to sweep home the only goal from 10 yards in the 74th minute.
Lennon started with a 4-1-4-1 formation with Stokes on the left and Ki Sung-yueng and Joe Ledley supporting centre-forward Gary Hooper.
Ki in particular found a lot of space in front of Aberdeen's back four but the Dons frustrated the visitors before Foster lost the ball in his own half.
The Celtic manager said: "We made it nervous for ourselves because we had so many chances and our decision-making on the final bit was poor.
"We worked the ball great, kept getting in between their midfield and back four and then we tried to walk the ball in the net at times.
"It's a bad habit to have and we have to get out of it. I said at half-time we needed to be patient, we would take 1-0 and that happened to be the case.
"But I felt our play deserved better, overall we were very, very good."
Lennon, who lost left-back Emilio Izaguirre to a broken leg in the first half, added: "I didn't think we toiled, we were just wasteful in the final third.
"We worked the ball to Kris in good positions on numerous occasions and we kept failing.
"But we kept going and Kris is always a threat and he did brilliantly for the goal."
Lennon claimed his players were guilty of over-elaborating in training too but he added: "I'm not overly concerned, we always felt we would score with the players we have in the team."
The Irishman had just moved Stokes into the middle before his goal after bringing on James Forrest for Joe Ledley, but he was planning another change.
Lennon said: "We were thinking of taking Stokesy off, believe it or not, so it shows you how much I know, and maybe getting Paddy (McCourt) in a wider area.
"We worked the ball really well into the wider areas and just needed an eliminator to pick the right option, and Paddy is very good at that.
"But thankfully we got the goal before we made the substitution."
Foster thought he was fouled when Commons slid in to make the crucial challenge, although it looked a fair challenge and referee Calum Murray generally allowed play to flow.
Aberdeen manager Craig Brown said: "I think we did enough to get at least a point.
"We actually just committed suicide towards the end of the game, it was a careless error that cost us the game.
"Some think it might have been an infringement but I would need to see it again."
When asked if Foster claimed the challenge was illegal, Brown said: "He thought it was a foul but he would think that."
Scott Vernon had a good chance in either half, Lukasz Zaluska blocking his first effort following a counter-attack, before the Englishman failed to make meaningful contact with Darren Mackie's low cross.
"I think we actually made the best chance of the game when (Josh) Magennis headed on to Mackie who crossed across the face of goal and if Scott Vernon had got a touch it might have been a different result," Brown said.
"We were a bit depleted and I thought the lads who played gave us a shift and didn't deserve to lose."