Roberto Di Matteo's side moved four points clear of second placed Manchester United, who host Tottenham in Saturday's late game, thanks to Mata's second half winner after Gervinho had cancelled out Fernando Torres's opener.
Inevitably, Chelsea captain John Terry had to endure taunts from Arsenal fans after this week's FA verdict that he was guilty of racially abusing QPR's Anton Ferdinand in a Premier League match last October.
But Terry had the last laugh as Chelsea, unbeaten in the league this season, secured their first win at the Emirates Stadium since November 2009 and handed the Gunners their first league defeat of the campaign.
The Blues took the lead in the 20th minute when Spain forward Torres produced an instinctive close-range volley from Mata's free-kick.
After a slow start, Arsenal finally found some momentum towards the end of the half and equalised in the 42nd minute.
When Alex Oxlade-Chamberlain whipped in a low cross from the right flank, Chelsea's defenders were caught too deep and Ivory Coast striker Gervinho took advantage of the space with a quick turn and blistering finish into the roof of the net.
But Mata put the European champions back in front as the Spanish midfielder's 53rd minute free-kick curled across the penalty area and glanced in off Arsenal defender Laurent Koscielny.
Source: AFP
Source: AFP