Arteta's side moved five points clear at the top with goals from Mikel Merino and Bukayo Saka, stretching their unbeaten run in all competitions to 18 matches, but the Arsenal manager said the victory "came at a cost".
Arsenal, already without centre-backs Gabriel Magalhaes and William Saliba, lost another defender when Cristhian Mosquera limped off shortly before half-time. Arteta then watched Declan Rice, who had delivered another dominant midfield display, pull up with what appeared to be a calf issue in the closing stages.
"We have to see what Declan has got," Arteta said. "He can walk, but he cannot play. He has played a lot of minutes for us. The schedule has been incredibly demanding and we had one less recovery day than Brentford.
"We played on Wednesday night and then again on Saturday lunchtime. It is not ideal. These players need more time to recover."
Arteta rested Saka, Jurrien Timber and Eberechi Eze after facing Tottenham, Bayern Munich and Chelsea inside seven days, but his rotated line-up still delivered an eighth straight home win.
The opener came after just 11 minutes. Fit-again Noni Madueke combined sharply with Ben White, whose precise cross found Merino. The midfielder's header bounced into the turf and beyond Caoimhin Kelleher for his 12th goal of the season in all competitions.
David Raya, facing his former club, made a superb save to tip Kevin Schade's header on to the bar as Brentford threatened briefly, but Arsenal controlled the majority of the contest. Rico Henry twice denied Madueke before half-time with crucial last-ditch challenges.
Brentford improved after the interval and introduced Igor Thiago, the league's second-highest scorer, but Arsenal regained control once Arteta introduced Eze and Saka. Calafiori and Rice tested Kelleher from distance before Merino dragged a rebound wide.
Saka eventually settled the match in stoppage time, staying onside to drill in a low strike that looped over the Brentford goalkeeper's hand. It was his 10th goal of the league campaign and confirmed Arsenal's 10th league win of the season (W10, D3, L1).
The defeat left Brentford with only one away league victory this term. Bees manager Keith Andrews said he remained encouraged by his players' effort.
"We conceded an early goal and we should have done better with that," Andrews said. "But we grew into the game and made it uncomfortable for them. I am proud of the performance."
Arsenal's win maintained their unbeaten home league record and extended Arteta's run against Brentford to nine matches without defeat. But the Arsenal manager's focus now shifts to the fitness of Rice and Mosquera ahead of Saturday's trip to Aston Villa, another match arriving with little time for recovery.
Enzo Maresca admitted that Cole Palmer's long-awaited return was "the only good news" on a punishing Wednesday night for Chelsea, who were beaten 3-1 by a sharp Leeds United side at Elland Road.
When Thomas Frank returns to face Brentford, now as manager of Tottenham Hotspur, the stakes could not be higher.
Liverpool were held to a 1-1 draw by Sunderland at Anfield after a late own goal rescued a point for the Premier League champions.
Arsenal manager Mikel Arteta has acknowledged the growing strain on his league-leading squad as several key players face uncertain fitness ahead of Wednesday evening's clash with Brentford.
