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 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 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.”
It wasn’t all good news for Celtic though as left-back Emilio Izaguirre suffered a broken leg after going down in agony following a sliding challenge from Peter Pawlett.
Lennon said: “It’s a huge blow for us to lose him and we don’t know how long he is going to be out for.
“He is being assessed at the minute and we’ll know whether he requires surgery and, if he does, he will be out for three months anyway.”
Lennon held his head in his hands when he was told the initial diagnosis that Izaguirre had suffered a suspected fracture.
“You can always tell by a player’s reaction and Emilio is not a player to feign injury,” Lennon said.
“So the concern was immediate and he was taken into the dressing room and looked at and the word came out it was a fracture.”
Elsewhere yesterday Motherwll beat Hearts 1-0 to top.
On Saturday Irishman Jon Daly was on the scoresheet as Dundee United drew 1-1 with St Mirren while Dunfermline and Inverness finished 3-3.