Logan Forsythe set up the winning hit with a one-out single against Hector Rondon (2-1). He moved up on a groundout before Alexi Amarista was intentionally walked.
Hundley then lined a clean single into center field and Forsythe scored easily, giving San Diego its third win in the last four games. Dale Thayer (2-3) wiggled out of a jam in the top half to get the victory.
The game lasted 5 hours, 13 minutes, and the teams used 15 pitchers total. But it wasn't even the longest game of the weekend: Arizona beat Philadelphia 12-7 in 18 innings Saturday night.
Each team had a chance to win the game in extra innings before Hundley came up with his clutch hit.
The Cubs grabbed the lead with two runs in the 13th inning. They loaded the bases with no outs, and Darnell McDonald came home when first baseman Jesus Guzman fielded a grounder and threw it off Nate Schierholtz's helmet as he tried to make it to first.
Brian Bogusevic then hit a sacrifice fly, but Junior Lake struck out and Donnie Murphy flied out to end the inning.
The Padres responded in the bottom half. Guzman doubled and scored on Ronny Cedeno's two-out triple. Cedeno then came home with the tying run when closer Kevin Gregg uncorked a wild pitch.
San Diego looked poised to end the game in the 14th when it put runners on second and third with one out. But Eric Stults, batting for fellow pitcher Brad Boxberger, struck out swinging while facing a five-man infield and Chase Headley looked at a called third strike to end the inning.
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Chicago then wasted its own opportunity to go in front. It loaded the bases with one out in the 15th, but Lake grounded into a fielder's choice that cut down Starlin Castro at home and Murphy grounded out.
It was easy to see why each team has struggled this year. The Padres (59-71) are in fourth in the NL West, while the last-place Cubs (55-75) have dropped 11 of 14.
Both of the clubs wasted a solid start.
Chris Rusin allowed three hits and walked four in 6 1-3 innings for Chicago, lowering his ERA to 2.64. The left-hander is 0-2 in his last three starts despite a 2.00 ERA.
San Diego right-hander Andrew Cashner pitched seven innings of two-hit ball against his former team. The 6-foot-6 righty struck out seven and walked one.
NOTES: Cubs C Welington Castillo was back in the lineup after missing three games with bruised ribs. ... Cubs 1B Anthony Rizzo will remain in the No. 2 spot in the order. Rizzo, according to manager Dale Sveum, has sparked the offense the last four games. "We're scored six, four, six and three," Sveum said before Sunday's game. "I'm not changing anything." ... The Padres will start Tyson Ross on Monday when they open a two-city, six-game road trip in Arizona. ... The Padres aren't sure on their starting pitcher on Wednesday. With veteran RHP Edinson Volquez's recent release, the Padres are juggling their rotation and considering various options.
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