The in-form Spain international landed awkwardly late in the 3-0 victory at Upton Park on Tuesday night after scoring twice.
Negredo scored a hat-trick in the first leg at the Etihad Stadium and was the scourge of struggling West Ham once again as he struck in each half to take his tally to 23 goals for the season.
Fit-again Sergio Aguero was also on target as City coasted to a 9-0 aggregate win, but the sight of Negredo in pain in the latter stages of the match prompted concern from boss Manuel Pellegrini.
"Alvaro Negredo has a problem with his shoulder. He just has a pain at the moment, and we will see how it is tomorrow." the Chilean told Sky Sports.
Some dreadful West Ham defending made City's victory all too easy and the Premier League title-hopefuls are now unbeaten in their last 18 matches - winning 16 of those.
Pellegrini was able to reflect on a job well done once again as City booked a final meeting against either arch-rival Manchester United or Sunderland in March.
He said: "It was a very professional performance. It was easy to think the game was finished from the 6-0 in the first leg, but it was important to reach the final winning all the games.
"For Sergio Aguero, it was a useful match as he played 60 minutes. For him, it was useful for the future.
"Wembley is always important. It was important the way we reached the final, winning every game."
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