The Portuguese midfielder was taken off on a stretcher after an awful forearm challenge from Ben Thatcher sent him crashing into the advertising hoardings at the City of Manchester Stadium. After a lengthy stoppage Mendes appeared to be unconscious as he was taken away and Thatcher was lucky to escape with only a yellow card.
City's disappointing start to the season continued as they have picked up only one point from a possible six and, although they were the better side they rarely threatened in front of a crowd of 37,214, their lowest league attendance at their new home.
City were without suspended striker Bernardo Corradi, sent off during Sunday's loss at Chelsea, while manager Stuart Pearce dropped midfielder Ousmane Dabo. This helped to accommodate Darius Vassell and Paul Dickov as the new front pairing with £6million striker Georgios Samaras switched to the left of midfield to give City more balance on that side.
Pompey promoted Kanu, who scored twice in Saturday's 3-0 win, to the starting line-up at the expense of Svetoslav Todorov.
Midfielder Joey Barton was City's most effective attacking weapon, having his side's first two attempts on goal.
Barton played a great return pass with Vassell, crashing a shot narrowly wide and then fired another long-range effort straight at keeper David James.
Richard Dunne thumped a drive wide and a Samaras header looped over James but luckily for Pompey fell on the roof of the net as City made a lively start.
Pompey had little to offer in the opening period. Gary O'Neil shot harmlessly wide after being set up by Kanu and as City's frustration increased Trevor Sinclair was booked following a wild challenge on Matthew Taylor.
There was controversy early in the second half with the Thatcher and Mendes incident which resulted in a four-minute stoppage before play resumed.
And moments later City wasted one of their best chances of the night when Claudio Reyna released Vassell who shot narrowly wide from just inside the box when he should have hit the target.
City were rarely troubled, although they were indebted to keeper Nicky Weaver after 68 minutes when he made a brilliant block to keep out Taylor's shot, their first on target effort of the game.
City sub Ishmael Miller made an immediate impact after replacing an ineffective Samaras. The young striker had a terrific shot from the edge of the penalty area which James did well to parry.
Pompey had Sean Davis booked for a clumsy tackle on Dickov - their first caution of the game on 76 minutes.
City huffed and puffed in the latter stages but were unable to blow a hole in the Pompey defence which comfortably dealt with everything thrown at them.
And deep into the four minutes of stoppage time, Pompey could easily have won it. Right back Glen Johnson made a weaving run in to the penalty area but luckily for City his cross took a deflection which took it away from the oncoming Portsmouth players.
And as the final whistle sounded the City players left the field to a chorus of boos as the fans vented their anger following a forgettable display.