The City Manager called off the pound pair after little over an hour, an indication of his displeasure of their desperately poor performances.
In the eight matches in which they have been paired together, Anelka and Fowler have each only found the net once.
And earlier the week it earned a rebuke from Keegan who told the pair they must do better.
The introduction at Maine Road legend Shaun Goater and Jon Macken, who replaced the out of form frontmen was greeted with the loudest cheer of the afternoon.
Though Goater and Macken were unable to conjure a match winning goal, they at least brought the crowd alive and inspired a marginally more spirited show in the last half hour.
But Keegan was left to reflect on another dreadful display as City have won only once in their last eight matches, the worst spell in Keegan's career in management at Newcastle, Fulham and City.
It was a further indication of their attacking woes that young midfielder Joey Barton had their only 2two shots on target in the first three quarters of the match.
Barton, who was making his only second start for City, earned his second man of the match award and outshone many of his more illustrious team-mates.
Middlesbrough who extended their unbeaten run to eight league matches weren't any better as they only once troubled City keeper Peter Schmeichel.
The only shot the Dane had to save in a mind-numbingly bad 90 minutes came 14 minutes from the end.
Brazilian Juninho made a lively break from midfield and released Malcolm Christie on the left of the penalty area, but his weak effort was easily saved by Schmeichel.