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Castro drove a 1-0 fastball from Zach Miner (0-1) to the center field batter's eye for his eighth homer. The leadoff drive through a steady wind was his first homer since July 31 against Milwaukee and gave Chicago a 4-3 lead.
"I've been kind of struggling," Castro said. "It's been a long time since that happened, so I'm pretty happy."
Castro went 2-for-5 for his second consecutive multihit game. The shortstop is batting a career-low .242, but the homer against the Phillies was one of his hardest-hit balls this year.
"If he can put that kind of swing on that ball to center with the wind blowing in, that was nice and that's your game winner" Cubs manager Dale Sveum said. "Balls are coming of the bat like it did a couple of years ago and last year."
Michael Young collected three more hits for Philadelphia, which has split its last six games. Young went 4-for-5 in the Phillies' 6-5 victory in Friday's series opener and is batting .588 (10-for-17) in four games against the Cubs this season.
Kevin Frandsen homered for the second straight day, giving him five on the year, but Philadelphia dropped to 9-7 under interim manager and former Cubs second baseman Ryne Sandberg.
Carlos Villanueva (3-8) pitched 1 1/3 innings for the win and Kevin Gregg got three outs for his 28th save in 33 chances. Five Cubs relievers combined for four innings of two-hit ball.
"Villanueva got four huge outs and then you can match up to get to your setup guy and closer and set what happens," Sveum said.
"Obviously (home wins) haven't been coming around too much lately," he added. "So it was nice to get the lead and all the relievers did a great job and we made the plays when we had to."
It turned into a battle of the bullpens after left-handers Cliff Lee of the Phillies and Chris Rusin of the Cubs each allowed three runs, two earned, in five innings.
Gillespie drove in Castillo with the last of three consecutive singles in the second, tying it at 1. Castillo had a tying RBI single in the third, and Gillespie's sacrifice fly in the fifth made it 3-3.
Lee allowed nine hits, struck out four and walked three. The 2008 AL Cy Young Award winner is 1-4 with a 3.98 ERA in his last eight starts.
"He just seemed a little out of sync the whole start, throwing a lot of pitches, missing just off the plate," Sandberg said "He's a guy that usually pitches ahead in the count and goes after it and pounds the zone."
Lee agreed that it was an odd day for him.
"It was a strange game in the fact that they waited out some pitches that were right there just out of the strike zone and they were being called ball consistently," Lee said. "It didn't seem like I ever got a good break as far as them chasing a good pitch."
Frandsen gave the Phillies the lead with a line drive to left in the second, and Carlos Ruiz had a run-scoring double in the third after first baseman Anthony Rizzo committed a costly two-out error.
Young made it 3-2 in the fourth with an RBI triple that got past Gillespie in the right-field corner. He also had a tiebreaking RBI single in the ninth inning in the series opener.
But Young also committed an error in the third that led to Castillo's tying hit.
Phillies OF Domonic Brown struck out swinging in the ninth as a pinch hitter. The All-Star slugger was out of the starting lineup after he left the series opener due to soreness in his right Achilles tendon. "I'm probably going to feel it the rest of the year," Brown said. ... Philadelphia 3B Cody Asche (right hamstring strain) was ready to return to the lineup, but Sandberg decided to give him another day with a lefty pitching for the Cubs.
Copyright by STATS LLC and The Associated Press
CHICAGO, IL - AUGUST 31: Cliff Lee #33 of the Philadelphia Phillies pitches against the Chicago Cubs during the...