When the former Northern Ireland international replaced Steve Kember at Selhurst Park in December, Palace were 19th in the table and facing a relegation battle.
But after scraping into the play-offs on the last day of the regular season thanks to Brian Deane's last-gasp goal for the Hammers at Wigan Athletic, Dowie's side will be playing in the Premiership in August, for the first time since
their relegation six years ago.
Palace deserved their victory as they created the better chances in a tight match.
After a scrappy opening, Palace's Danny Butterfield drifted a sixth minute free-kick inches wide before Wayne Routledge's cross was headed over the bar by Andy Johnson.
The game opened up midway through the first half as Shaun Derry's free-kick was deflected just wide in the 18th minute before Danny Granville completely miskicked the ball after Stephen Bywater has misjudged a corner.
Two minutes later Bobby Zamora ran clear of the Palace defence but Nico Vaesen blocked the former Brighton and Spurs striker's shot with his legs.
Bywater then did well to save Johnson's 22nd minute shot before the match degenerated into a scrappy affair again although Christian Dailly did head a good chance wide for Alan Pardew's side on the half-hour.
In the 38th minute Tomas Repka kicked Michael Hughes' effort off the line after Bywater had done well to partially block the shot.
The second half started nervously with both sides desperate not to make a crucial error but on the hour Vaesen made a solid save to stop Steve Lomas' goalbound volley.
However, Palace scored the winner two minutes later when Bywater could only parry Johnson's shot and the predatory Shipperley was on hand to fire the rebound into an empty net.
It was a simple but priceless goal by the much-travelled 29-year-old who is enjoying his second spell with Palace.
Shipperley has played for Southampton, Nottingham Forest, Barnsley and Wimbledon since starting his career with Chelsea but he will never score a more important goal.
Almost immediately David Connolly and Zamora had efforts disallowed for offside but Palace threatened to add another goal on the break as Pardew's side ran out of ideas.
Tommorow in the Second Division Play-Off Final between Bristol City and Brighton, Town will find out the 24th and final team who will make up Division One next season.
Live Coverage of the Match can be found on ITFM Matchday Live from 3PM.