The Lancashire all-rounder made a career-best 145 to push his side towards a declaration at 447 for 9.
Graeme Swann, Dean Cosker and Darren Thomas then claimed a wicket apiece as Gauteng closed the second day at the Wanderers Stadium still 168 runs short of avoiding the follow-on.
There was an early disappointment for the tourists in the second over of the morning when Worcestershire's Vikram Solanki went to pull a short ball from the left-arm pace bowler Ross Veenstra only to drag the ball on to his stumps having made 24.
Swann included a quartet of well-timed fours in his brief innings of 18 before reaching wide outside off stump to touch a ball from Veenstra to first slip.
Chris Read then joined Flintoff in a seventh-wicket partnership which added 91 in 19 overs.
Flintoff reached his hundred off 140 balls in 222 minutes, including 14 fours and a six, and boosted the scoring rate sufficiently to enable the England A captain Michael Vaughan to declare in mid-afternoon.
Read was out for 38 but Flintoff then really cut loose and surged past his previous highest first-class score of 124 made against Northamptonshire last June.
At this stage Gauteng were forced to deploy a field with no fewer than eight men patrolling the boundary.
Flintoff was finally caught on the deep midwicket boundary off Zander de Bruyn having lofted the bowler for a straight six the previous ball. He had been in for 276 minutes, faced 176 balls and hit 18 fours and two sixes.
There was still time for Thomas to stroke three fours before Paul Franks was out, after which Vaughan called a halt to set Gauteng a follow-on target of 298.
The pitch looked flat when the Gauteng batsmen began their reply until the introduction of the England spinners changed the complexion of the innings.
Swann tempted the opener Adam Bacher to sweep but the out-of-favour Test player went so far across his stumps that he was bowled behind his body for 13.
Two more wickets then fell with the score on 91, with Sven Koenig trapped leg-before by Cosker one short of his 50 before Andre Seymore went back to Thomas next over only to see the ball drop down and roll on to his stumps.
It was left to Derek Crookes and De Bruyn to play out time against Swann and Cosker, both of whom were getting appreciable turn.
Second day of three; England A won toss
ENGLAND A - First Innings
(Overnight: 263 for 4)
A Flintoff c Crookes b de Bruyn 145
V S Solanki b Veenstra 24
G P Swann c Crookes b Veenstra 18
C M W Read lbw b de Bruyn 38
P J Franks c Bacher b de Bruyn 8
S D Thomas not out 14
Extras (b2, lb1, w2, nb17) 22
Total (for 9 dec, 129.2 overs) 447
Fall (cont): 5-272, 6-310, 7-401, 8-431, 9-447.
Did not bat: D A Cosker.
Bowling: Veenstra 25-7-57-2; Kidwell 21-1-83-1; De Bruyn 22.2-6-81-3; Masimula 13-4-43-0; Crookes 24-4-84-0; Bodi 22-2-87-3; Bacher 1-0-4-0; Koenig 1-0-5-0.
GAUTENG - First Innings
S G Koenig lbw b Cosker 49
*A M Bacher b Swann 13
A J Seymore b Thomas 21
D N Crookes not out 19
Z de Bruyn not out 17
Extras (b3, lb3, nb5) 11
Total (for 3, 49 overs) 130
Fall: 1-31, 2-91, 3-91.
To bat: G Toyana, N Pothas, R E Veenstra, G Bodi, E W Kidwell, W B Masimula.
Bowling: Thomas 11-2-23-1; Franks 10-2-26-0; Swann 12-3-37-1; Cosker 11-4-23-1; Flintoff 5-1-15-0.
Umpires: B Lambson and C Schoof.Reuse content