The Portuguese champions could have fallen behind after just 10 minutes when Alex Telles tripped Aleksey Miranchuk inside the penalty area, but Iker Casillas pawed away Manuel Fernandes' resulting spot-kick.
A Moussa Marega penalty and Hector Herrera header put them two up before more haphazard defending – this time from Eder Militao – allowed Anton Miranchuk to reduce the deficit.
Jesus Manuel Corona put the result beyond doubt after 47 minutes, though, as Porto moved onto seven points at the summit of Group D.
While admitting his side were good value for their second consecutive Champions League win, Conceicao warned his players that they need to sharpen up at the back.
"It was a game in which we were superior, there is not the slightest doubt of that," he told a media conference.
"We controlled the game and had more possession of the ball, but each time they recovered the ball and attacked, we suffered.
"I forgive all sorts of errors, but a lack of concentration is annoying.
"There are situations that we must avoid, like leaving ourselves constantly exposed."
Casillas – the competition's record appearance holder – paved the way for his side's win with his penalty save and, like his coach, believes it was a deserved three points.
"I was lucky to make that save on the penalty and it was a bit incredible how it happened as we were controlling the game and suddenly Lokomotiv had two chances that stunned us," he said.
"We got to 2-0, which was fair and deserved and then in another strange play they scored. In the second half we started stronger and in the end it is a fair result."
Defeat leaves Lokomotiv rooted to the bottom of the table without a point, but coach Yuri Semin insists his beleaguered side should take comfort from the fact they carved out a host of opportunities.
"We had a great first half, created so many opportunities throughout the game and that's the positive we should take from this game," he said.
"But of course, we should never waste them like we did."