An early goal from Edin Dzeko proved the difference between the teams, in a match shortened to 80 minutes after heavy rain in Hong Kong prior to kick-off had waterlogged the pitch.
As a result of their triumph, City will now prepare to face Sunderland in the final of the 2013 Barclays Asia Trophy friendly tournament, which will take place on Saturday.
Pellegrini, who was returning to the dugout having missed City's last friendly outing due to the death of his mother, named a familiar-looking starting XI containing only one recent signing in the form of midfielder Fernandinho.
His team subsequently started with encouraging fluency, as Dzeko twice went close, the latter opportunity seeing the Bosnian narrowly fail to convert a James Milner cross.
But that combination paid dividends moments later, with the tall striker making no mistake as he headed home a cross from the former Leeds United midfielder to put his side 1-0 to the good.
The goal-mouth action largely dried up prior to the end of a truncated first half, but Pellegrini took the unusual step of making just one substitution - with Aleksandar Kolarov replacing Gael Clichy at left-back.
A further flurry of changes followed after the interval, but barring a Fernandinho clearance off the line and a clash of heads involving Micah Richards, fans at the Hong Kong Stadium had little to get excited about in the second half.
City will take on Sunderland next after they beat Tottenham 3-1 earlier on Wednesday.
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