Vick went 15-of-30 through the air for 208 yards and an interception in his return after missing three games with broken ribs.
The Eagles (5-8) scored all of their points in the second quarter as Philadelphia's defense forced Miami into a trio of miscues. They also stopped the Dolphins twice on third and fourth down in the decisive frame.
The Eagles defense added a safety with a fourth-quarter sack of quarterback J.P. Losman in the Miami end zone.
The Dolphins (4-9), who came into the contest winning four of the five, allowed a total of nine quarterbacks sacks Sunday.
Starter Matt Moore was sacked four times and Losman was tackled five times for a loss of 38 yards.