Sri Lanka were 39 for one in their second innings when bad light stopped play on the third day.
Chaminda Vaas and
England's plight would have been worse as they slumped to 205 for seven before battling innings by Graham Thorpe (57) and Gareth Batty (38) frustrated Sri Lanka.
Left-arm paceman Vaas started an England collapse in the morning as three wickets fell for 28 runs, before mopping up England's tail with the new ball to finish with four for 77 from 24.2 overs.
Muralitharan took two more wickets to finish with four for 60 from 40 overs.
Thorpe provided the main resistance for the tourists, playing Muralitharan skilfully and working the ball into the gaps with characteristic industry, to top score with a four-hour innings lasting 198 balls.
The left-hander was well supported by Batty, with whom he added 51 runs in 174 balls for the eighth wicket, halting England's early morning slide.
When Thorpe was pinned in front of his stumps by Muralitharan's leg break, Batty continued the tourists' rearguard resistance with a 23-run partnership with Ashley Giles (16).
Sri Lanka finally took the new ball in the 111th over of the innings with instant success. Vaas found the edge of Giles's bat in his first over and Batty then skied a pull as he tried to score some quick runs.
Batty had batted for nearly three hours and faced 159
England lost their first wicket of the fourth over when Paul Collingwood (28) edged an off-cutter to end a 58-run stand for the fifth wicket with Thorpe.
Flintoff, dropped on four by Dinusha Fernando, smote two fours and one enormous six before edging an attempted lofted drive against Muralitharan on to his stumps via his pad.
Chris Read was lbw for a duck soon after to leave England tottering on 207 for seven before the last three wickets scratched 87 useful runs.
Sri Lanka first innings 382 (T.Dilshan 63, D.Fernando 51; A.Giles 5-116):
England first innings (overnight 163-4)
M.Trescothick c Dilshan b Muralitharan 36
M.Vaughan c Jayawardene b Muralitharan 52
M.Butcher st Sangakkara b Dharmasena 4
N.Hussain lbw Vaas 10
G.Thorpe lbw Muralitharan 57
P.Collingwood c Sangakkara b Vaas 28
A.Flintoff b Muralitharan 16
C.Read lbw Jayasuriya 0
G.Batty c Dilshan b Vaas 38
A.Giles c Jayawardene b Vaas 16
J.Kirtley not out 3
Extras (b-16 lb-10 nb-8) 34
Total (all out, 114.2 overs) 294
Fall of wickets: 1-89 2-100 3-119 4-119 5-177 6-202 7-205 8-256 9-279
Bowling: Vaas 24.2-4-77-4, Fernando 7-0-36-0 (nb-5), Dharmasena 19-3-63-1 (nb-3), Muralitharan 40-18-60-4, Jayasuriya 24-6-32-1
Sri Lanka second innings
M.Atapattu lbw b Giles 8
S.Jayasuriya not out 25
K.Sangakkara not out 1
Extras (lb-5) 5
Total (for one wicket) 39
Fall of wicket: 1-33
Bowling: Kirtley 7-2-15-0, Flintoff 5-1-11-0,
Giles 3-1-8-1, Batty 1-1-0-0.