Jayawardene made 126 not out as Sri Lanka, set 262 for victory, finished on 265 for two to inflict what was England's 13th defeat in 17 One-day internationals.
Together with wicket-keeper Kumar Sangakkara (58 not out), Jayawardene shared an unbroken third-wicket stand of 140 in 155 balls as Sri Lanka won with nearly eight overs to spare.
England stand-in captain Andrew Strauss had said before the start of the series that if his team scored five individual hundreds they'd be successful.
But, unfortunately for him, Jayawardene's innings meant he'd witnessed a century in each match from a Sri Lanka batsman with England no nearer ending their woeful One-day form in the run-up to next year's World Cup in the Caribbean.
England, who'd bowled 43 wides in the previous two matches, only sent down five this time but more than compensated with a series of loose deliveries.
"As a side, individually and collectively, we've got to have a long, hard look at ourselves," Strauss told reporters afterwards. "If we're honest, we haven't been up to international standard so far this series and we've been comfortably the second-best team.
"We know we can play a lot better than we have done and it's up to us to find a way to do it," added Strauss, captain in the absence of Michael Vaughan and Andrew Flintoff.
For Sri Lanka, on a roll since squaring the Test series 1-1 at Trent Bridge earlier this month before winning the one-off Rose Bowl Twenty20 clash, this was a significant victory with the bulk of their previous success in the sub-continent.
"That was probably the best game we've played out of the three," said an elated Jayawardene. "I think our bowlers bowled really well and when chasing a score it's important one of the guys makes a big hundred and it was my day today. I'm very happy with that.
"This is very big. The whole tour has been hard for us. When we came here a lot of things were said about us being a young side," Jayawardene, captain in place of Marvan Atapattu, whose back injury prevented him coming to England, added. "Our guys worked really hard and it's paying off now."
Sri Lanka got off to a flyer after Ian Bell's patient 77 had been the cornerstone of England's 261 for seven.
Sanath Jayasuriya, fresh from his 122 in Sri Lanka's 46-run second One-day international win at The Oval on Tuesday, cashed in against Stephen Harmison and Liam Plunkett, both playing on their Durham home ground.
Plunkett's first two overs went for 17 runs but England's plight was summed up by the fact that Sajid Mahmood, his replacement, had conceded 80 runs in seven overs at The Oval.
However, Mahmood struck first ball to run out Jayasuriya for 23.
With Sri Lanka 88 for one off 11 overs, medium-pacer Collingwood, the third Durham player on show, faced another rescue operation just as he'd done when coming to the crease with England 92 for three.
Upul Tharanga, who'd made a century in Sri Lanka's 20-run series-opening win at Lord's, gave his wicket away on 41.
But that was as good as it got for injury-hit England with Jayawardene's 16th four, off Harmison, seeing him to a 104 ball-century.
Earlier, England again lost early wickets with dangerman Kevin Pietersen caught behind for six.
The umpires later refused England a substitute fielder for Pietersen, ruling he had a pre-existing injury after taking a blow on the knee at The Oval.
Bell, on the ground where he scored a Test-best 162 not out against Bangladesh last year, was run out in the penultimate over having faced 114 balls with three fours.
Such was Sri Lanka's control that star off-spinner Muttiah Muralitharan, who'd left the tour to be with his ill son, was barely missed.
The series continues at Old Trafford on Wednesday and concludes at Headingley a week on Saturday.