With the Cubs trailing 2-1 in the sixth, Rizzo led off with a triple. One out later, Kris Bryant hit a liner to shallow center that Matt Szczur made a running catch on and fired home to get Rizzo for the inning-ending double play - the fourth San Diego double play to that point behind starter Clayton Richard.
Hedges got the ball early and moved to apply the tag. Rizzo didn't slide and sort of dropped down to his knee as he crashed into the catcher, who tumbled backward. Hedges had to leave the game with a bruised right thigh.
''I think you look at that play and it's a fairly egregious violation of the rule,'' San Diego manager Andy Green said. ''The rule exists to protect the catcher. The safety of the catcher is more in jeopardy now when you have the rule to protect you because you're not expecting to get hit when you give a guy a plate like that.
''That's a cheap shot. I'm not saying he's a dirty player at all - nobody is saying that - but he clearly deviated from his path to hit our catcher, took our catcher out. Rule exists to protect him. It's a disheartening play to see come about like that.''
No one on the Cubs' side saw it that way.
''It's one of those plays where it's very sensitive,'' Rizzo said. ''It's a play where I'm out by two steps. If I slide, he runs into me.
''I've talked to a lot of umpires about this rule. It's my understanding if they have the ball, it's game on.''
Chicago manager Joe Maddon agreed with his star player.
''You don't see it anymore because the runner thinks he has to avoid (the catcher) - he doesn't,'' Maddon said. ''If the guy's in the way, you're still able to hit him.
''I'd much prefer what Riz did tonight. What he did was right, absolutely right. There's nothing wrong with that and nobody can tell me differently.''
Rizzo extended his career-high hitting streak to 13 games by going 2 for 3 with an RBI.
Jose Pirela and Yangervis Solarte each had a solo homer for the Padres, although Pirela's error allowed the winning run to score.
Hector Rondon (2-1) pitched a scoreless inning for the win. Davis had runners on second and third with one out, but struck out Wil Myers and got Hunter Renfroe to ground out for his 14th save in 14 chances.
Kirby Yates (1-1) allowed one unearned run to get the loss.
Szczur, claimed off waivers by the Padres from the Cubs last month, went 0 for 2 with a walk and a hit by pitch in his return to Wrigley Field.
Padres: RHP Trevor Cahill (right shoulder strain) is with the team, but is expected to leave for a rehab assignment in the next few days.
Cubs: SS Addison Russell (sore right ankle) and OF Jason Heyward (left hand abrasion) didn't start. Russell, though, entered in a double switch at the start of the seventh. . 2B Ben Zobrist (left wrist) is eligible to come off the 10-day DL on Friday, but is uncertain if he'll be ready. ''I'll probably see how it feels on Wednesday,'' Zobrist said. ... LF Kyle Schwarber left the game after fouling a ball off his right ankle. X-rays were negative.
Cubs LHP Mike Montgomery (0-3, 2.56 ERA) goes in the middle game of the series and will face Padres RHP Jhoulys Chacin (6-5, 5.10).