Burnett (8-17) took over the major league lead in losses, and the defeat ensured Philadelphia (69-82) its second consecutive losing season.
When asked to characterize his disappointing year, Burnett was in no mood to discuss it.
"We'll describe it when the season is over," he said.
Amarista's two-out homer in the sixth inning followed a walk to Jake Goebbert and put the Padres ahead 4-3. Amarista, who doubled in the second and singled in the fourth, fell a triple short of the cycle when he grounded out in the eighth.
"I'm not going to make excuses," Burnett said. "I messed up. I walked a guy, and the curveball (to Amarista) wasn't down enough."
Phillies manager Ryne Sandberg also lamented getting beaten by the lower portion of the lineup.
"A two-out walk and a two-run home run to bottom of the order guys," he said.
Burnett, who has gone 2-8 in his last 10 starts, gave up five runs — four earned — and eight hits in 5 2-3 innings. He also walked four batters to increase his major league-leading total to 87.
Burnett struck out four to pass Phillies Hall of Famer Robin Roberts for 43rd place on baseball's career strikeout list with 2,361.
Amarista, acquired by the Padres in a May 2012 trade with the Angels, has already equaled or surpassed his career highs in plate appearances, runs, hits, home runs and RBIs.
San Diego won its second straight game after dropping nine of 11. The Phillies have lost seven of 11.
Ian Kennedy (11-13) pitched six innings for the win. The right-hander allowed three runs and three hits with seven strikeouts and four walks. Kennedy had lost his previous two starts, giving up double-digit hits in both outings.
Freddy Galvis hit a two-run homer in the fifth inning to give the Phillies a 3-2 lead. Dominic Brown had a solo homer in the second.
Philadelphia, held to one hit by Andrew Cashner in a 1-0 loss on Monday night, managed just five hits against Kennedy and three relievers.
Phillies: SS Jimmy Rollins took infield practice but is still not expected back before the weekend. Rollins has been out since Sept. 8 because of a strained left hamstring.
Padres: OF Seth Smith missed the start due to a sore right hamstring, although he walked as a pinch-hitter. Smith tweaked his hamstring while making the final out on Monday. The left-handed hitting Smith isn't scheduled to start on Wednesday night with Phillies lefty Cole Hamels on the mound.
Phillies: Hamels (8-7, 2.51 ERA), a San Diego native, has had great success facing his hometown team with an 8-2 record and an ERA of 2.21 in 15 career starts.
Padres: LHP Eric Stults (7-16, 4.49) will try to avoid tying Burnett for the major-league lead with 17 losses.
JUST SHORT OF THE CYCLE — AGAIN
With Amarista missing the cycle, the Padres and Miami Marlins are the only teams in the majors to not have a player accomplish the feat. It was the 358th time, the Padres have had a player fall one hit short.
ANOTHER LOSING SEASON
The loss dropped Philadelphia to 69-82, ensuring the club's second consecutive losing season with 11 games remaining. It is also the third straight non-winning season after the team went 81-81 in 2012.
IT NEVER RAINS IN CALIFORNIA
With a rare summer shower that moved through San Diego in the late afternoon, although it missed Petco Park, the Padres issued a thunder alert. Early-arriving fans were cautioned to take cover until the alert was lifted 45 minutes before the game.
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