Bony struck late for the Swans but it was nothing more than a consolation as City kicked off 2014 in winning fashion.
"It's a very good result," Pellegrini told Sky Sports.
"Swansea are a strong team here, at home. Wherever they play they are a very strong team, so to win today is very important for us.
"I think that we had a very good first half - in control of the ball against a team that's very good in keeping possession.
"The goal at the end of the first half was offside. They drew level with that goal but at the beginning of the second half we continued trying to score the second goal.
"We scored the second and the third and it was a pity that they scored the last goal because I don't think 3-2 was the difference between the two teams. But we beat a good team today."
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