Humber got some good defense behind him and needed it in a duel with the Cubs' Matt Garza, who gave up just four singles in a complete game.
Garza held the White Sox hitless for 5 1/3 innings before Juan Pierre hit an RBI single in the sixth.
"I'm very fortunate," Humber said after his first career appearance against the Cubs.
"I was behind in the count a lot and just was able to throw something down in the zone when I needed an out. They made some great plays," he said.
"(Garza) was on his game. He's got great stuff. We knew it was going to be tough against him, but our guys battled and scratched across a run."
Humber (8-4) allowed five singles and is now 5-1 in his past six starts.
"If Phil Humber isn't on the All-Star team -- and he deserves to be on the All-Star team -- then there shouldn't be an All-Star Game because he's been that good for us, stepping in for guys who have been hurt and being the guy who's pitched well for us from day one," White Sox catcher A.J. Pierzynski said.
Cubs manager Mike Quade was ejected in the second inning for arguing a call at second on one of three double plays turned by the White Sox in the first three innings. Quade was tossed by second-base umpire Paul Emmel after protesting that White Sox second baseman Gordon Beckham didn't touch the bag on a pivot before relaying to first.
Matt Thornton pitched a perfect eighth and ninth for his third save in seven chances.
"I wasn't too happy. One of those things I was out of the dugout when the play was developing," Quade said. "I don't manufacture stuff. To me I just thought he was way off the base. That shouldn't be given."
The White Sox have now beaten the Cubs 15 times in their last 20 meetings and are 4-1 this season.
Beckham worked a walk leading off the sixth, moved up on Humber's sacrifice and made it to third on Garza's wild pitch. After a close 1-2 pitch was called a ball, Pierre slapped a single to left over a drawn-in infield for the White Sox's first hit and the first run of the game.
"I thought it was inside, but I was definitely holding my breath when he made the call," Pierre said.
"I was mad," Garza said of the pitch that wasn't called a strike. "Big situation, a big moment right there. I wanted that pitch. ... I should have put Pierre away."
Pierre said Garza was as tough as he's ever seen him.
"I haven't seen him that much, but his fastball was at 95-97 with three other pitches to go along with it. We scrapped, but it just goes to show you how good Humber was for us today," Pierre said.
"He was just as effective, Thornton coming in and closing it out. That's been the key this last week here is the pitching and bullpen just being lights out for us."
Pierre, who'd been criticized for his uneven play this season, came up with his third key hit in three games. He delivered a tiebreaking single to spark an extra-inning win over Colorado on Thursday and had a go-ahead two-run triple Friday in the White Sox's 6-4 victory.
"Opportunities have presented themselves and I've put a couple good swings on balls. That's about it," Pierre said. "About two or three weeks ago I was leaving guys on and now I'm getting the hits. ... It's a long season."
The Cubs grounded into double plays in each of the first three innings, spoiling any chance of an early offensive outburst against Humber.
"We had pitches to hit and didn't hit in some of those situations," Quade said.
They got the first two runners on in the first and second innings only to be turned away. And then in the sixth, Darwin Barney led off with an infield single off Humber's glove and Starlin Castro reached on a slow roller up the third baseline, again putting two runners on and no outs.
Humber then retired Aramis Ramirez and Carlos Pena on pops, threw a wild pitch to advance the runners and then retired Marlon Byrd -- who came off the disabled list before the game -- on a grounder.
Byrd returned to the lineup for the first time since he was hit near the left eye by a pitch from Boston's Alfredo Aceves on May 21, causing multiple facial fractures.
Byrd wore a protective flap over the left side of his batting helmet.
"Whatever happens, happens. Can't go out there with fear, not in this game," Byrd said. "The game is too fast."
He drew a four-pitch walk from Humber in his first at-bat in the second, following a leadoff single from Pena, who foiled a defensive shift with a bunt down the third base line. Byrd then rolled hard into Beckham who still got off the throw to first after Alfonso Soriano's grounder to third. That brought Quade racing out of the dugout to argue.
Castro hit into two double plays in the first three innings.
Game notes
Game-time temperature was 93 and it dropped 15 degrees in the first five innings with the wind blowing in. ... Adam Dunn got the start in right field in the NL Park. He went 0-for-4 with three strikeouts and is now 2-for-33 with 19 strikeouts over his past 10 games, with his average plummeting to .168. It was his second game in the outfield this season.
