In a match where much of the focus was on the large-scale police operation outside Villa Park, the hosts took victory thanks to goals from Ian Maatsen and Donyell Malen.
Maatsen opened the scoring on the stroke of half-time, with Malen doubling the lead from the penalty spot just before the hour mark.
But despite dominating for long spells, Villa also rode their luck with Dor Peretz missing two big chances for the visitors.
“It was a very good three points, not playing brilliant but playing serious and patient,” said Emery.
“We conceded more chances than we planned and made some mistakes.
“But overall in 90 minutes we dominated and managed the match getting the three points, while managing the players to get balance with the matches we are playing.”
The win was Villa’s third in four Europa League matches, moving them up to sixth in the table. Their next match is at home to Young Boys on November 27.
Emery continued: “I am happy because the performance was the most important.
“The performance, individually and collectively, maybe I am not happy completely.
“But I can understand with our way, the experiences we have in Europe previously, you can expect you are better than the opponent but you have to respect your opponent.”
More than 700 police officers were deployed on the streets for one of the most politically-charged matches the UK has ever seen.
With no Maccabi fans in attendance, protests took place outside the ground from both pro-Palestine and Pro-Israeli groups with six people arrested before kick-off.
Maccabi’s squad arrived at Villa Park five hours before kick-off on police advice, something which did not please their boss Zarko Lazetic.
"It was not normal," the Serbian said. "Sitting....nothing to do. (We came) Five hours before the match. It was very difficult. It was not our decision."