Steve Cotterill's men have yet to taste defeat in 10 League One matches this season and the leaders stormed into a 2-0 half-time lead courtesy of Agard's double, which included a penalty.
But visitors have also started the campaign well and Dean Bowditch halved the deficit six minutes into the second half before Benik Afobe levelled in the 73rd minute by capitalising on Wade Elliott's poor backpass.
However, City scored almost immediately from the kick-off as Elliott atoned for his error with a powerful drive that moved the hosts five points clear at the summit.
Peterborough United moved up to second with a 1-0 over Fleetwood Town.
Darren Ferguson's men had lost their last two league matches, but Conor Washington's strike on the stroke of half-time settled the contest at London Road.
Swindon Town routed Sheffield United 5-2 last Saturday and they continued their fine run with a 3-0 win at Barnsley.
All of the goals came in the second half with Nathan Byrne, Jake Reeves and Andy Williams on the scoresheet at Oakwell, as the hosts slipped into the bottom four.
Leyton Orient began life without Russell Slade with a 3-2 reverse at home to Rochdale, who moved into the top six despite having Ashley Eastham sent off.
Preston North End also entered the play-off spots thanks to a 2-0 success at Coventry City.
There was drama at Bramall Lane as two late goals saw Sheffield United defeat Gillingham 2-1.
Luke Norris put the visitors into an 83rd-minute lead, but Michael Higdon levelled for the hosts before Jamie Murphy secured the win in the seventh additional minute.
At the bottom end of the table, Colchester United won for just the second time in the league this season in a 3-0 success at rock-bottom Crewe Alexandra, while Scunthorpe United's early season woes continued in a 3-2 setback at Oldham Athletic.
Chris Lines' penalty was not enough for Port Vale to beat Bradford City as the two played out a 1-1 draw at Valley Parade.
Elsewhere, Chesterfield drew 1-1 with Notts County, Crawley Town defeated Yeovil Town 2-0 and Doncaster Rovers slipped to a 3-0 loss at Walsall.
