Latics were on course to finish fifth in the First Division after Neil Roberts fired them into a 1-0 lead at a packed JJB Stadium.
But a last-minute equaliser from Brian Deane gave the Hammers a share of the spoils and robbed Jewell's side of competing in the play-offs.
Other results went their way with Ipswich drawing against Cardiff and Crystal Palace losing at Coventry, but Deane's last-gasp strike left them in seventh spot, two points behind sixth-placed Palace.
Despite the cruel result, Jewell was full of praise for his players and has backed them to be battling up near the top again in 2004/05.
He said: "The lads have done the club proud, and while we haven't got into the play-offs, I offer a big thank you to them.
"They have learned a lot about themselves this season with many of them not having played at this level before.
"We certainly won't be going into unchartered waters next season, although the division could be harder as the sides coming down will be strong, and the ones coming up are good.
"However, with some improvement we can have another good go at it, and I hope we are going to be bigger and stronger next season.
"It doesn't necessarily follow – Nottingham Forest were in the play-offs last year yet had a relegation battle this time.
"But we will improve over the summer, not just by bringing in new players, but because the lads who are already here will be even better equipped for First Division football."
Latics were on top for most of the first half yesterday, Roberts' 34th minute goal their reward for launching wave after wave of attacks.
After the interval, though, West Ham started to come into their own, and there were a few hair-raising moments before Deane headed the equaliser.
Jewell said: "I feel empty inside, and I feel so sorry for the players. They were written off at the start of the season with some people even calling us relegation candidates.
"But yesterday we battered West Ham for 40 minutes but couldn't get the second goal which would have finished the game off.
"Considering all the pressure on the game, the performance in the first half was outstanding and it was only a second goal which was missing.
"Their keeper made a couple of good saves, we had a couple of chances which were off target with – West Ham weren't in the game in the first half.
"In the second half, they came more into this, we had to get our blocks in, and I thought we had weathered the storm.
"Their goal was a disappointing one to concede, but this isn't the time for an inquest.
"It does hurt that the other results went for us – if we had drawn and the other two had won, it wouldn't have been quite as bad.
"But because it happened so late here and the results went our way, it feels a lot worse."
Yesterday's crowd of 20,669 was a record football attendance at the JJB and Jewell was delighted with the huge turn out.
He said: "I would like to say a big thank you to the supporters and I'm just sorry they won't be able to watch us in the play-offs.
"They have taken a lot of stick from other clubs' fans, but not from us and certainly not from me."
Source: Wigan Evening Post.
From the Manchester Evening News:
Latics' anguish
By Neil Barker
BIG Brian Deane's dramatic last minute equaliser shattered Wigan's Premiership dream and turned cheers into tears for distraught home fans.
The party's over for Wigan - they're denied a place in the play-offs following their failure to beat The Hammers on a day when rival results went for them. Deane's header was a crushing blow for Latics who finish their debut season as a First Division club in seventh spot.
Wigan had one foot in the play-offs when Deane headed home a Michael Carrick free-kick. The result left Wigan manager Paul Jewell gutted. He told M.E.N. Sport: "To lose it so late is a real kick in the teeth. "I feel totally empty inside - the feeling gets worse and worse when you see other results going for you.
"This can be a cruel game. West Ham's goal was very disappointing. We were so close and I feel for all the players.
"We have come a long way and just missed out at the very end. It's not been a bad effort though considering we were labelled relegation certainties at the start of the season.
"We will be stronger next time round. We simply have to improve over the summer."
Salute
Jewell saluted his side's outstanding first-half performance. They battered West Ham and deservedly broke the deadlock on 34 minutes with a goal from Neil Roberts.
The 20,699 attendance was the biggest gate at a football match in Wigan for 50 years and home fans were counting the minutes down when Deane outjumped Jason De Vos and planted a simple header beyond John Filan. The damage was done there and then - Wigan were finished.
With Crystal Palace losing at Coventry, Wigan seemed to be on their way to the play-off but that man Deane had other ideas. Gary Teale fouled Marlon Harewood and Carrick's free kick found Deane's head - the stunned silence of the shell-shocked home fans told its own story.
Manager Jewell's pained expressions were equally visible after seeing a superb effort in which Jimmy Bullard and Leighton Baines were superb count for nothing.
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