Ricardo Quaresma's goal with a quarter of an hour remaining saw the Portuguese giants stay top of Group H.
Lopetegui was mostly pleased with his team's display, but said the key aspect was collecting all three points.
"We had some brilliant moments against Athletic and they are a great team, with a lot of technical quality," he said.
"This was a very good game in every respect. Athletic responded well and bounced back after the break, but the most important thing was that we managed to win."
Hector Herrera's opener just before half-time had Porto on track before Guillermo Fernandez cancelled out the goal.
Lopetegui believes "it will not be easy to finish on top" of the group as he praised Quaresma for his match-winner.
"I brought Ruben Neves on for Juan Quintero to freshen up the midfield, to put in some more physical strength and also to rest the player, who made a huge effort in the weekend game against Sporting," he said.
"Ricardo Quaresma – we are thrilled with him. He did what he was asked and gave us a lot of pleasure – and of course, the win."
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