Falcao had not scored in his previous three league games but put an end to his mini-slump in fine style.
A long pass from defense deflected off the back of midfielder Joao Moutinho and fell to Falcao. He sprinted into the penalty area down the right, beat the left back for pace and expertly chipped the ball over Lopes as he charged off his line.
"Falcao works hard for the team, he closes down, he holds the ball up," Monaco coach Claudio Ranieri said. "Everyone should try and play for him more."
Last weekend Lyon had relinquished a 2-0 lead away to relegation battlers Sochaux and again looked vulnerable to set pieces. Gomis scored in the 62nd when his header from left back Henri Bedimo's cross went in off the post.
Moments later, Yannick Ferreira Carrasco, who scored twice for Monaco against Sochaux, hit the post with a shot from just inside the penalty area. At the other end, Lyon went close to equalizing in the 80th when Jimmy Briand's shot shaved the woodwork.
"We did well to hold onto our lead," Ranieri said. "The important thing is to keep the ball and slow the game down."
Even though the performance was better in the second half, it is proving a tough season for seven-time former champion Lyon, which has won only two of its past 14 matches in all competitions.
"We missed tackles, we were off the pace, including me," Lyon midfielder Clement Grenier said. "Our first half was very average. We just sat back and watched them play, for some reason."
Earlier, center forward Cheick Dibate and winger Ludovic Obraniak scored late goals as Bordeaux beat 10-man Montpellier 2-0.
It was Bordeaux's second win in three games and moved it up to 13th place, while Montpellier is 15th.
Montpellier was up against it after Yassine Jebbour was shown a straight red card in the 18th minute for a dangerous high tackle on Lucas Orban.