Unai Emery's men have now won 15 consecutive Premier Leagues at Villa Park and back-to-back victories over Manchester City and the Gunners have sparked hopes of an unexpected challenge for their first title since 1981.
The only goal came after just seven minutes when Villa captain McGinn span onto Leon Bailey's cross and fired into the top corner.
"What a monumental week it has been for us," said McGinn.
"That was actually a really tough spell for us we played Thursday, Sunday, Wednesday, Saturday and I think it showed in our performance tonight, it wasn't our best, but I'm certainly not complaining.
"The second half was a bit of character, a bit of grit and fair play to the substitutes who've come on."
Arsenal's second league defeat of the season leaves Mikel Arteta's men one point behind Liverpool, who went top with a controversial 2-1 win at Crystal Palace earlier on Saturday.
Arteta was forced to watch from the stands as he served a touchline ban and had to restrain himself after the game when asked about a couple of controversial incidents.
Arsenal thought they should have had a penalty in the second half when Gabriel Jesus went down under a challenge from Douglas Luiz.
And Kai Havertz had a late goal disallowed for handball.
"I do (have a) big opinion, yes," said Arteta. "(But) I prefer not to comment."
Victory was sweet for Emery, who was sacked by Arsenal four years ago.
The Spaniard has made a remarkable impact at Villa, since his return to England over a year ago.
"It was a tough week and now after these three points we have to be happy but also keep balance," said Emery.
"I will speak again when we are in game 32 or 33. Today we are at game 16 and we are not a contender (for the title)."
Arsenal rue lack of killer striker
Arsenal were left to rue a number of big missed chances that raise fresh doubts over whether they can win a first Premier League title in 20 years without a natural goalscorer.
"We were the better team, we didn't deserve to lose but this is football," said Arteta.
"(Scoring is) the only thing we miss today. We created some really big chances."
Arsenal's first big chance came even before Villa scored as Bukayo Saka failed to make contact with Gabriel Martinelli's cross.
Seconds later, they were behind as McGinn took a perfect touch from Bailey's cross to tee up his fifth goal of the season.
Emiliano Martinez ensured Villa's lead lasted until the break as he denied Martin Odegaard and Jesus.
Arteta endured a frustrating watch as Villa rode their luck in the second half.
Ollie Watkins turned a corner onto his own post before Odegaard wasted another big chance by skewing wide.
Saka did finally find a way past Martinez, only to be flagged offside.
And there was late drama when Havertz outmuscled Matty Cash to bundle in at the back post.
The ball appeared to come off both players' hands as they battled for possession, but the referee's decision to award handball against Havertz was confirmed after a lengthy VAR review.
Arsenal's defeat opens the door for fourth-placed City to close back to within four points of the top when the English and European champions visit Luton on Sunday.
