Birmingham - Sri Lanka proved too strong with both ball and bat as they beat England by six wickets in the fifth and final one-day international at Edgbaston on Tuesday to clinch a 3-2 series victory.
First paceman Lasith Malinga took three for 50 as Sri Lanka restricted England to 219 all out.
Then, after Sri Lanka had wobbled at 62 for three, fifties from Mahela Jayawardene (53) and Lahiru Thirimanne (60 not out), together with captain Angelo Mathews's 42 not out off 34 balls, saw the tourists home with 10 balls to spare.
But there was a controversial moment during England's innings when Sachithra Senanayake ran out Jos Buttler as the non-striker backed up.
Mathews upheld the appeal for a perfectly legitimate dismissal and Buttler, whose blistering 121 had so nearly taken England to victory in the fourth ODI at Lord's, was out for 21.
"You would have to ask Angelo Mathews," said Cook when asked for his view of the run out during the presentation ceremony.
"We were obviously disappointed. I hope I wouldn't do it.
"You don't know in the spur of the moment how you would handle it."
However, Mathews insisted: "He was taking starts, not only this game but in the last game as well.
"We gave him two warnings, and I don't know what else you can do to stop him doing that, so we had to go for it.
"I would stick by it. What we did was completely within the rules. We warned him in the last game too."
Sri Lanka, set a seemingly modest 220 for victory, were cruising at 55 without loss in the eighth over as Tillakaratne Dilshan got after the England seam attack.
But their charge was interrupted by off-spinner James Tredwell's burst of two wickets for four runs in 11 balls.
First he had Dilshan, whose 28 featured five boundaries, caught off a flashing drive by Joe Root at extra-cover.
Tredwell struck again when Kumar Sangakkara, the century hero of Sri Lanka's seven-run fourth ODI win at Lord's on Saturday, was caught on two at slip by Chris Jordan.
Then spearhead James Anderson had Kusal Perera lbw.
Star batsman Jayawardene had made just eight when he edged left-arm paceman Harry Gurney between wicketkeeper Jos Buttler and first slip Jordan, neither going for a chance that probably belonged to the gloveman.
Left-hander Thirimanne hooked Ravi Bopara just short of Gurney at long leg before Jayawardene's delicate late cut, with the ball almost in Buttler's gloves, off the medium-pacer went for four.
But Jayawardene was out for 53, ending a fourth-wicket stand of 98 when he skied all-rounder Jordan to Anderson at mid-off.
Sri Lanka were now 160 for four in the 39th over.
Thirimanne pressed on to an 89-ball fifty before Anderson dropped a return catch when the batsman was on 58 - although by then Sri Lanka were in sight of victory.
Off-spinner Senanayake, allowed to take part under International Cricket Council regulations despite being reported for a suspect action at Lord's, again proved economical in taking one for 36 from 10 overs.
He had arguably observed the 'spirit of cricket' by warning Buttler before running him out.
Nevertheless, Senanayake was roundly booed by the crowd, who considered his run out of Buttler unsporting.
It was the eighth recorded instance of a player being dismissed this way in an international match (four each in Tests and one-dayers) since Australia's Bill Brown fell victim to India's Vinoo Mankad in the Sydney Test of 1947/48 - hence the term 'Mankading' which is used to describe the practice of a bowler running out a non-striker backing up.
Regardless of Buttler's dismissal, England's top-order batted poorly after Cook won the toss.
Left-handed opener Cook top-scored with 56 in an innings where the only other batsmen to get out of the 20s were Ian Bell (37) and Jordan (30).