Reynolds singled home Upton with two outs in the bottom of the ninth inning as the Diamondbacks rallied to edge the San Diego Padres 6-5.
"We discussed it a little bit before my at-bat in case he came up and it just worked out for us," said Upton, who went 1 for 3 with two runs and three RBIs.
Upton drew a two-out walk from Cla Meredith (4-2) and stole second base before Reynolds lined a single into the left-field corner.
"He told me that he was going to steal if I got a ball," Reynolds said. "I got a ball and he stole second. That's what we planned in the dugout. It's pretty cool."
It was a script Meredith had hoped to avoid.
"You don't want to let one guy in the lineup beat you and right now, Upton's that guy," Meredith said. "Rather than staying hard and going after him, I lost my aggressiveness trying to throw him off-speed stuff, fell behind, he walked and the rest is history."
Jon Rauch (1-0) pitched the ninth for the Diamondbacks, who have won three straight for the first time since May 20 through 23.
"Three in a row feels good," Diamondbacks manager A.J. Hinch said. "We've put together a decent momentum stretch. It wasn't always easy, but we found a way to hang in there."
Tony Gwynn Jr. went 4 for 5 with a stolen base and a run scored for the Padres, who lost for the fifth time in six games.
Kevin Kouzmanoff snapped a 3-3 tie in the seventh with a double off the left-field wall that scored Gwynn from second. Everth Cabrera made it 5-3 in the eighth as he walked, stole second, then stole third and scored when catcher Miguel Montero's throw sailed past Reynolds into left field.
Arizona cut the deficit to 5-4 in the eighth when Montero doubled and scored on Gerardo Parra's single to center. Luke Gregerson, activated from the 15-day disabled list earlier Monday, retired Tony Clark on a double-play grounder before Tracy hit his third career pinch-hit homer over the right-field fence.
"I was looking for a fastball middle and he gave me a fastball middle," said Tracy, who homered for the first time since coming off the disabled list with a strained right oblique. "Pinch hitting is the hardest game in baseball, no doubt about it."
Upton gave the Diamondbacks a 1-0 lead in the first off Walter Silva with a sacrifice fly. San Diego scored two in the second on four singles, an error and a wild pitch.
Upton made it 3-2 in the bottom of the third with a two-run homer off the batters' eye above the center-field fence. Adrian Gonzalez tied it when his RBI single scored Cabrera, who had led off with a walk.
San Diego manager Bud Black also credited Upton with saving at least three runs on defense with a pair of running, backhand catches in the right-center field gap.
"What you saw were speed plays with Upton," Black said. "If those balls fall, we still have guys on base, we get extra bases, not an out's made and who knows what happens?"
Jon Garland, winless in nine starts since May 19, allowed three runs on eight hits over six innings with two walks and four strikeouts.
Silva lasted just 3 1/3 innings, allowing three runs on seven hits with a walk and a strikeout.
The crowd of 17,528 was the second-lowest in franchise history. ... Garland is 0-2 with three no-decisions and a 3.06 ERA in his last five starts. ... Before the game, the Padres placed infielder David Eckstein on the 15-day disabled list with a strained right hamstring and activated Gregerson from the 15-day disabled list. Eckstein pulled up lame running out a grounder in the 12th inning of San Diego's 7-6 loss Sunday to Los Angeles in 13 innings. ... Gregerson had been on the disabled list with a strained right shoulder. ... San Diego also recalled RHP Mike Ekstrom, who threw 2 2/3 innings of scoreless relief, and optioned LHP Joe Thatcher to Portland. ... RHP Ryan Webb, acquired by the Padres from Oakland on Sunday in a four-player trade, reported to the team and was in the bullpen Monday.