Gareth McAuley's early header looked to have lifted Ipswich off the foot of the table, but Ellington had the final say at Portman Road.
Ipswich remain the only club in the English leagues to be without a win, while Watford are now unbeaten in six matches away from Vicarage Road.
Keane's side needed an early goal to settle their nerves and it arrived after only four minutes when Liam Rosenior's cross was headed back across goal by Jon Walters and McAuley planted a header into the back of the net.
Things almost got even better less than two minutes later with Rosenior again providing the cross which Pablo Counago should have headed home before Lee Martin's strike hit the crossbar.
John Eustace had an opportunity at the other end but the experienced midfielder headed straight at on-loan goalkeeper Asmir Begovic.
But Ipswich continued to look threatening going forward and it took an agile save from Scott Loach to deny Spanish striker Counago.
On-loan midfielder Henri Lansbury had a chance to equalise but the midfielder dragged his right-footed strike wide of the target.
Winger Carlos Edwards spurned a chance to double Ipswich's lead when he flashed a shot wide from the edge of the area nine minutes before the break.
Adrian Mariappa had the first opportunity of the second half when Lansbury's cross picked him out, but the Watford defender's header drifted wide of the upright.
Edwards was causing problems for the Watford defence and England Under-21 goalkeeper Loach produced a fine save with his feet to keep out the former Sunderland man's right-footed drive from 12 yards out.
Watford boss Malky Mackay brought on Ellington in a bid to add some firepower but the Hornets remained on the back foot and Town substitute Connor Wickham came close with a header from David Wright's cross that looped narrowly wide.
Ellington had his first sight of goal 17 minutes from time, but the former Wigan frontman failed to get any power on his long-range strike and Begovic made a comfortable save.
McAuley had a chance to score his second goal of the night but the central defender headed an Edwards cross over the bar from close range.
The impressive Loach was again called into action to deny Wickham and Tommy Smith late on to set up a nervy finish.
And with time running out, Ellington slotted home Danny Graham's cross from six yards to silence the Ipswich faithful.