Steven Thompson scored two goals in three minutes late in the first half to give Saints the advantage.
A 77th minute strike from Bob McHugh put the Saints under pressure, but Lennon's men held on to secure the win.
Lennon, who revealed David Barron, Gary Teale and Paul Dummett all went off with muscle problems, said: "I'm delighted with the victory and the overall performance. Motherwell are fantastic at what they do.
"I must give (Motherwell boss) Stuart (McCall) and his staff great credit for the way that they play. They are very, very open and very bold at times and they go for things.
"They leave themselves two v two at the back and the last 20 minutes they put us under severe pressure down the flanks with the fantastic pace that they have.
"That was something we had to consolidate. I thought we had a very good 60 minutes in terms of owning the ball and creating. The chances and work rate were exceptional.
"But also we showed a great resilience and a defensive mentality, that we won't be broken, and we were delighted to get over the line."