Arrieta (2-1) allowed three hits and overcame three walks, striking out four en route to the victory.
Welington Castillo drove in a pair of runs while Starlin Castro, Darwin Barney, Anthony Rizzo, Ryan Sweeney and Luis Valbuena each added an RBI for the Cubs, who took the rubber match of a three-game set.
Phillies starter Kyle Kendrick (10-12) was tagged for five runs on eight hits over six full innings.
Darin Ruf homered for the Phils.
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