Arenado's two-run shot in the first inning made him the second player in club history to hit 40 or more homers in three different seasons. Vinny Castilla hit a career-high 46 in 1998 to cap a three-year run of 40 or more.
Arenado joins Castilla, Eddie Matthews and Mike Schmidt as the only players to have three 40-homer seasons while playing predominantly third base.
''It's pretty cool. They have longevity in this game, they were able to compete for so long and I have the utmost respect for them,'' Arenado said. ''To be with them in that category is cool but I've got a long ways to go to get to that level.''
Arenado has hit 18 homers since Aug. 1, most in the majors, and extended his on-base streak to 18 games during which he is hitting .419.
After a July slump the All-Star has found his groove late in the season.
''I train to be able to compete in October,'' he said. ''I feel like I've had my second wind in August and I feel great. My energy's up.''
Jeff Hoffman (2-6) got his first victory since May 29 against Arizona, allowing four runs on four hits in 5 1/3 innings. He walked two of his six batters in the first inning but began to settle down after the second inning.
''I told him after the game his last 40 pitches were better than his first 50,'' Rockies manager Bud Black said. ''He battled, I loved how he competed. We picked him up but he kept battling. Good for him.''
Hoffman got plenty of help from his defense. Arenado caught a scorching liner from Eric Hosmer and doubled up Greg Garcia to end the first and Garrett Hampson made a leaping catch at the wall in center to rob Garcia of extra bases in the third.
''Hos crushes the ball to third, turns into a double play. Kind of let (Hoffman) off the hook there,'' San Diego manager Andy Green said. ''If that shoots by Arenado, it's a different feeling baseball game.''
Story and Hampson hit back-to-back shots in a five-run fourth to make it 8-2, but the Padres sent 11 batters to the plate in the sixth to get within one.
Story hit a solo homer in the sixth, his 32nd, to make it 9-7. San Diego scored in the seventh and the Rockies added a run in the eighth.
Jairo Diaz got the final three outs to pick up his fourth save of the season and his third in the last four games.
Austin Hedges hit a two-run homer, his 11th, in the second for the Padres.
San Diego starter Joey Lucchesi (10-8) was roughed up for eight runs on nine hits through 3 2/3 innings. He left in the fourth after Story and Hampson homered.
''I came in here with confidence. I feel super comfortable here,'' Lucchesi said. ''I thought it was going to go my way, but it didn't.''
Padres: OF Hunter Renfroe remained out with a right ankle injury that has limited him to one appearance and no starts since Sept. 4. Green said Renfroe had hoped to play in this series. ''Been a slow process, he's frustrated not being able to play here,'' Green said.
Rockies: LHP Kyle Freeland (left groin strain) is scheduled to throw his third bullpen since going on the 10-day injured list on Aug. 22. Trainer Keith Dugger said Freeland would throw two simulated innings.
Colorado outfielder David Dahl was putting together a solid season when a high right ankle sprain on Aug. 2 landed him on the IL. Black confirmed Friday that Dahl won't be back this season.
The 25-year-old Dahl has dealt with injuries throughout his career, including one to his rib that cost him all of 2017. He finished 2019 hitting .302 with 15 home runs in a career-high 100 games and was named to his first All-Star Game.
''The numbers speak for themselves. I wish it could've been through the end of the year and it really could've been something,'' Black said. ''But that's a lot to build on. That was a very solid year.''
Padres LHP Eric Lauer (8-8, 4.41 ERA) will face RHP Peter Lambert (2-6, 6.86) on Saturday night. Lauer has a 19.73 ERA in three career starts at Coors Field, and Lambert is looking for his first win in his last 16 starts.
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