England set 279 to win, were bowled out for 217 with four overs to spare.
Fast bowler Ravi Rampaul led the attack with four for 41.
Chanderpaul had moved up from No 5 after top-scoring for the West Indies with 53 not out during their 79-run defeat in Sunday's series opener at Lord's.
Together with Marlon Samuels, dropped on 14 by Paul Collingwood, the England captain, off his own bowling on his way to 77, he put on 175 for the third wicket in 34 overs.
However, England appeared to have weakened their bowling significantly by omitting Monty Panesar.
This left them without a frontline spin bowler – Panesar's replacement Michael Yardy was given just six overs – which meant their attack lacked both variety and control.
England were 30 for two inside seven overs after Alastair Cook holed out to mid-off against Daren Powell and Ian Bell, on his Warwickshire home ground, was lbw to Rampaul although the ball appeared to be going over the top.
Matt Prior and Kevin Pietersen played some typically aggressive shots as England reached fifty.
But when dangerman Pietersen was out for nine, bowled middle-stump by Rampaul as he aimed legside, England were 64 for three.
Prior completed a 71 ball-fifty, his first at this level, with one six and three fours.
But two balls later, on 52, he chipped Daren Powell to Devon Smith, running round from mid-wicket in gathering gloom.
Eight balls afterwards England were 117 for five. Collingwood, who'd just avoided a Fidel Edwards bouncer the previous delivery, was lbw for one to a full-length ball from the quick in an intelligent piece of bowling.
Owais Shah and Yardy shared a stand of 54 without threatening the run-rate before the latter pulled Dwayne Bravo to Dwayne Smith at deep square leg.
And the game was up for England when, five balls later, 171 for six became 172 for seven after Shah, on 45, edged a pull off Rampaul to wicket-keeper Denesh Ramdin.
Earlier, Chanderpaul's hundred was only his seventh in 219 ODIs.
The 32-year-old Guyanese had been a thorn in England's side during the hosts 3-0 Test series success, averaging 148.66, and this was another example of his ability to pace an innings after he took 10 balls to get off the mark. In all he faced 122 balls with three sixes and 10 fours.
The series concludes at Trent Bridge on Saturday.
Scoreboard
WEST INDIES:
C.H. Gayle c Anderson b Sidebottom 36
D.S. Smith c Prior b Anderson 17
S. Chanderpaul not out 116
M.N. Samuels c Sidebottom b Broad 77
D.R. Smith lbw b Broad 7
R.S. Morton c Bell b Sidebottom 3
D. Ramdin not out 2
EXTRAS (LB-5, W-15) 20
TOTAL (for five wkts, 50 overs) 278
FALL OF WKTS: 1-50, 2-67, 3-242, 4-257, 5-274.
DID NOT BAT: D.J. Bravo, R. Rampaul, D.B.L. Powell, F.H. Edwards.
BOWLING: Anderson 10-3-78-1 (4w); Sidebottom 9-1-56-2 (3w); Broad 10-0-49-2 (2w); Mascarenhas 10-1-31-0; Collingwood 5-0-30-0; Yardy 6-0-29-0 (2w).
ENGLAND:
A.N. Cook c Edwards b Powell 19
M.J. Prior c D.S. Smith b Powell 52
I.R. Bell lbw b Rampaul 2
K.P. Pietersen b Rampaul 9
O.A. Shah c Ramdin b Rampaul 45
P.D. Collingwood lbw b Edwards 1
M.H. Yardy c D.R. Smith b Bravo 19
A.D. Mascarenhas c Powell b Rampaul 3
S.C.J. Broad c Ramdin b Edwards 22
R.J. Sidebottom run out 15
J.M. Anderson not out 3
EXTRAS (LB-10, W-13, NB-4) 27
TOTAL (all out, 46 overs) 217
FALL OF WKTS: 1-23, 2-30, 3-64, 4-113, 5-117, 6-171, 7-172, 8-179, 9-195.
BOWLING: Rampaul 10-0-41-4 (1nb, 2w); Powell 10-0-45-2 (3w); Edwards 10-0-43-2 (3nb, 3w); D.R. Smith 9-0-54-0 (1w); Bravo 7-0-24-1.
RESULT: West Indies won by 61 runs.
UMPIRES: N.J. Llong (England) and B.G. Jerling (South Africa).
TV UMPIRE: N.A. Mallender (England).
MATCH REFEREE: M.J. Procter (South Africa).
MAN-OF-THE-MATCH: Shivnarine Chanderpaul.
FIRST MATCH: Lord’s, England won by 79 runs.
THIRD MATCH: Trent Bridge on Saturday.—AFP