But a play at the plate that stopped Rizzo from scoring a run raised ire from the Padres and shrugs from Rizzo and the Cubs.
Rizzo tripled to open the Cubs sixth, bolted for home after Kris Bryant's liner to center was caught. Rizzo barreled into Padres catcher Austin Hedges after he caught a throw from center fielder Matt Szczur and defended the plate.
"It's a cheap shot," said Padres manager Andy Green. "I'm not saying he's a dirty player, nobody's saying that (but) he clearly deviated from his path to hit our catcher. He took our catcher out."
But the Cubs first baseman, who was tagged out on the play, said it was just good, hard baseball.
"By no means do I think that's a dirty play at all," Rizzo said. "I went pretty much straight in. He caught the ball and went towards the plate so I went in -- I slid in there -- it was a hard slide. ... I play this game hard for a 162 games-plus so I can't see that being dirty."
Hedges apparently suffered a bruised thigh in the collision and did not return for the seventh inning.
"I don't expect him to play tomorrow," said Green. "I don't know how long he's out for."
Javier Baez went 2-for-3 and scored a go-ahead run on a throwing error as the Cubs (35-34) beat the Padres for the first time this season after three losses last month in San Diego.
Reliever Hector Rondon (2-1) worked one inning -- a scoreless seventh -- for the victory.
Right-handed reliever Kirby Yates (1-1) took the loss after allowing one run on two hits in the seventh.
Cubs reliever Wade Davis faced five batters in the ninth and had runners on second and third with one out after two wild pitches. But he struck out Wil Myers swinging and got Hunter Renfroe to ground out to earn his 14th save.
The Padres (28-43) dropped their second straight and third in four games despite homers from leadoff batter Jose Pirela and second baseman Yangervis Solarte.
Rizzo, playing this sixth game in the leadoff spot, extended his hitting streak to a career-high 13 games. He has reached base in all six games leading off, just the fifth Cubs player to do so since 1946.
Lester worked six innings and allowed two runs on five hits. He walked one and struck out seven.
The Cubs tied the game 2-2 in the seventh on Willson Contreras' sixth homer of the season, coming with none out on Richard's 1-2 pitch.
Richard departed with one out, and Baez greeted Yates with a single to shallow right. Albert Almora Jr. then doubled to left, and Baez scored on Pirela's throwing error for a 3-2 Cubs lead.
Richard allowed two runs on five hits over 6 1/3 innings. He walked three and struck out three.
The Padres claimed an instant 1-0 lead on leadoff batter Pirela's first-inning home run. Pirela sent Lester's 1-1 pitch to center field for his third homer of the season.
In the bottom of the first, Rizzo spoiled the Padres' infield shift toward first base by placing a perfect bunt down the third-base line that wasn't picked up until he had reached first.
"It's not your prototypical lead off the game," said Rizzo.
Solarte made it 2-0 in the third with a first-pitch homer to left field. It was his 10th of the season and third since Saturday, when he clubbed two against the Milwaukee Brewers.
The Cubs got one run back in the third when Rizzo sent a one-out sacrifice fly deep to left field to drive in Almora from third.
Chicago had runners at first and second with none out in the fifth, but Lester struck out while bunting foul and Jon Jay grounded into an inning-ending double play.
The Cubs were without right fielder Jason Heyward, who sat out Monday after suffering a laceration to his left hand in the second inning of Sunday's game at Pittsburgh while attempting to make a sliding catch.
NOTES: San Diego designated RHP Zach Lee for assignment on Monday and claimed LHP Dillon Overton off waivers from Seattle and optioned him to Triple-A El Paso. ... San Diego needs just one win this week to take the season series from Chicago after the Padres recorded a three-game sweep and held the Cubs to 12 collective hits last month at Petco Park. ... The Padres will send RHP Jhoulys Chacin (6-5, 5.10 ERA) against Cubs LHP Mike Montgomery (0-3, 2.65 ERA) in Tuesday's middle game. ... The three-game Cubs-Padres series is also Chicago's shortest homestead of the season. After Wednesday's finale, the Cubs embark on an 11-day, 11-game road trip that takes them to Miami, Washington and Cincinnati. ... The Cubs have been at the .500 mark 14 times this season. ... 1B Anthony Rizzo led off for the sixth time on Monday and went 2-for-3 with a bunt single and triple.