Saints led thanks to two goals in three minutes from Steven Thompson late in the first half before the introduction of Bob McHugh kick-started Motherwell's attacking play.
McHugh finished off the third of a hat-trick of chances in the 77th minute to put Saints under pressure, but they survived some tense moments.
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."
McCall could not criticise his side and was incredulous they failed to take a point. Paul Dummett twice blocked from Jamie Murphy after McHugh's goal and the visitors also had three penalty appeals turned down by Iain Brines, all for handball, twice on David Barron and once when the ball struck Jim Goodwin.
McCall said: "I thought it was great entertainment and a terrific game. They took their chances, two terrific goals from Steven Thompson, a near-post finish and a back-post clinical header.
"I was disappointed to go in at half-time 2-0 down. It was an open game, we had opportunities and hit the woodwork, and failed to hit the target on other opportunities.
"The last 30 minutes was just a siege, they brought big (Lee) Mair on, brought (David) van Zanten on. I don't think they could have brought any more defenders on. How we never got an equaliser I'll never know. But I said to the boys, there are ways to lose games and I certainly want to go down fighting."