With the draw in the three-match series, Mahela Jayawardene-led Sri Lanka overtook New Zealand to occupy the sixth place while England's failure to avoid defeat at Trent Bridge saw it lose one rating point.
Flintoff's men are now 19 points behind Australia and just one point clear of third-placed India, which is in a commanding position against the West Indies in the first Test at Antigua.
India held the second spot in the ICC Test Championship table in December last year after a 2-0 series win against Sri Lanka but dropped to the third place after 0-1 loss to Pakistan.
Sri Lanka, meanwhile, gained two rating points as a result of the shared series, secured by a 134-run win at Trent Bridge yesterday that canceled out England's six-wicket win at Edgbaston.
The series stalemate, which also included a drawn first match at Lord's, has lifted Sri Lanka to 97 points and level with New Zealand, but it moved above the Black Caps and into sixth place when the figures were re-calculated to three decimal places.
Sri Lanka is now just four rating points behind fifth-placed South Africa, according to an ICC release here.
For England the news is not so pleasing. It was the third series in a row since last summer's Ashes success against Australia it failed to win and that failure has cost the side one rating point, seeing it slip to 112.
The gap between England and Australia, which tops the LG ICC Test Championship table, has been extended to 19 points and it also means the margin between England and third-placed India is now just one rating point.
And while England now have a run of ODIs ahead of a Test series against Pakistan that starts in July, India can maintain the pressure on the side immediately above it if Rahul Dravid's line-up can string together a succession of victories in the ongoing four-Test clash with the West Indies.
LG ICC Test Championship: 1. Australia (131) 2. England (112) 3. India (111) 4. Pakistan (109) 5. South Africa (101) 6. Sri Lanka (97) 7. New Zealand (97) 8. West Indies (72) 9. Zimbabwe (27) 10. Bangladesh (3)