Sri Lanka, looking to square the series at 1-1 after England won the second Test at Edgbaston by six wickets, lost three wickets for two runs in 16 balls to go from 84 for two to 86 for four at lunch on Friday. Tillakaratne Dilshan was not out.
A stand of 82 between left-handers Upul Tharanga (34) and wicket keeper Kumar Sangakkara (36) kept England at bay for most of the session after debutant Jon Lewis had struck in his first over in Test cricket.
Flintoff had Sangakkara caught by wicket-keeper Geraint Jones although replays suggested the batsman had missed the ball. But the disbelieving keeper had to go after striking five fours in 76 balls.
Jones was in the action again when Hoggard had Tharanga caught behind and Flintoff then had Sri Lanka counterpart Mahela Jayawardene, who'd won the toss, taken by the Kent keeper for a three-ball nought.
Sri Lanka's first innings failures had plagued them all series and they continued when 30-year-old Gloucestershire seamer Lewis, in for the dropped Sajid Mahmood, struck with his third legitimate ball.
Lewis had left-hander Michael Vandort, who scored a battling hundred at Edgbaston, playing on for one after he got an inside edge to an attempted coverdrive.
Sangakkara was lucky not to be given out caught behind first ball down the leg side for nought off a thin glance against Lewis. However, together with Tharanga, he soon found his touch, both batsmen striking crisp offside boundaries.
Flintoff restored order by bowling round the wicket and repeatedly beating the outside edge before his breakthrough.
Sri Lanka recalled former skipper Sanath Jayasuriya, who arrived on tour during the drawn first Test at Lord's after the veteran left-hander ended his Test retirement following persuasion by recently-appointed chairman of selectors Asantha de Mel.
The 36-year-old, normally an opener, was listed to come in at number seven after Sri Lanka dropped out-of-form middle-order batsman Thilan Samaraweera. Medium pacer Nuwan Kulasekara was also omitted, Chamara Kapugedera taking his place.