"You program yourself," Burnett said after coming within two outs of his team's first complete game this season. "You want to finish what you started."
Burnett (4-6) gave up four hits and three walks with five strikeouts in 8 1/3 innings to improve to 5-0 in his career at Wrigley Field. He had a shutout until Alfonso Soriano's two-run home run to left with one out in the ninth ended a string of 18 straight scoreless innings by Pirates pitchers.
"It was the only ball that hung," Burnett said of the shot by Soriano. "He did with it what you're supposed to do with it. I go back a long way with Sori. ... I've gotten him a few times, he's gotten me.
"But you know, you can bury that pitch right there and I've buried it."
Burnett held the Cubs hitless until Nate Schierholtz's double down the line in right leading off the fifth. He threw 112 pitches and left after Soriano's home run.
Burnett did not want to come out after allowing a single to Anthony Rizzo before Soriano's home run, and despite a mound conference, manager Clint Hurdle said he had no intention of removing his starter until 115 pitches or some runs scored.
"You've got to give men an opportunity to do certain things no matter where you are or who it is, and he's earned that opportunity," Hurdle said. "There's been many games he's given us everything he's had."
Burnett threw a one-hitter in his last start at Wrigley Field last July 31. He lost the no-hitter in the eighth inning with two outs in that outing.
"It's a good place," Burnett said. "It's a good environment. A day game, too.
"You come to Chicago and Wrigley Field, even as a Marlin I enjoyed coming here a long time ago. So it's fun to get out and play against these guys on their field in their stadium."
Soriano's homer was the 379th of his career, tying him with Orlando Cepeda and Tony Perez for 64th on the all-time list.
But it was the Pirates doing almost all the hitting, as they gave Burnett some rare run support: They had scored three runs or less in six of his previous seven starts.
"The last couple times we haven't given him many runs," Alvarez said. "I don't care how good you are, it's always nice to pitch with some runs behind you."
The Pirates tagged Cubs starter Jeff Samardzija (3-7) for eight hits, including Alvarez's two-run home run in the fourth, his team-high 13th of the year. The right-hander struck out seven and walked one in six innings.
"The splitter was up all day today," Samardzija said. "(They) got a couple of hits off of it. Alvarez's home run was off of it.
"They took advantage of (the splitter) up in the zone and they made me pay."
Martin's homer, a two-run shot in the eighth off reliever Hector Rondon, was the 100th of his career.
The Pirates jumped on Samardzija for a run in the second on Garrett Jones' double and Alvarez's one-out RBI single. Pittsburgh added a run in the third when Starling Marte ended a streak of 14 hitless at-bats with a single, stole second and came in on Travis Snider's single.
Alvarez homered to right field after Martin led off with a walk in the fourth to increase the Pirates' lead to 4-0.
In the eighth, Martin sent a 3-2 pitch by Rondon into the seats in left for a two-out home run after Andrew McCutchen had drawn a walk.
Pittsburgh beat Chicago for the fifth straight time and handed the Cubs their fifth loss in the last six games overall.
"It's hard to see those guys play the way they play and we cannot play like that," Soriano said. "Especially, we got shut out yesterday. I don't want it to happen today again. At least he didn't throw a shutout."
Pittsburgh RHP Jeff Karstens, on the disabled list since March 26 with a shoulder inflammation, had surgery Friday on his right rotator cuff and labrum in Los Angeles. He'll be able to begin a rehab process in 10 to 12 weeks. ... The Pirates placed RHP Jared Hughes on the 15-day disabled list with a throwing shoulder inflammation and recalled OF Alex Presley from Triple-A Indianapolis. Presley had been sent down Monday when Hughes was called up. Hughes has returned to Pittsburgh for more evaluation. ... Cubs pitcher Kyuji Fuikawa, who went on the 60-day DL May 27 with a muscular strain in his right forearm, is expected to have surgery Tuesday after an exam on Monday. ... Cubs SS Starlin Castro, dropped from second to seventh in the order on June 4, continued to struggle. He went 0 for 3 and is mired in a 3-for-34 slump. ... Sunday's pitchers: Pittsburgh left-hander Jeff Locke (5-1, 2.45) vs. Chicago right-hander Edwin Jackson (1-8, 6.29).