"Coming back in that game is something special," said Guillen, who called Halladay one of the American League's best. "I never thought we'd rally like that. I thought it would be tough for us."
Konerko went 3-for-3 with two walks after missing a game with a bruised left arm.
"When you go down 3-0 and have Halladay on the mound, to rally is big," Pierzynski said.
Troy Glaus hit two homers for the Blue Jays, who have a season-high six-game losing streak -- their longest since losing six straight from July 9-18, 2004. It was Glaus' fifth multihomer game of the season and 23rd of his career. Glaus has 30 homers this season, seven behind his total for Arizona last season.
Garland (12-3) hasn't lost since June 8, at Detroit -- a span of 11 starts.
Garland settled down after allowing Glaus' homer in the first. He allowed three runs and eight hits in six innings -- lowering his ERA to 4.99. He struck out two and walked none.
"To be able to come back off Halladay is something we can build off. It will build our confidence," Garland said.
Toronto returned home after a 2-8 road trip that manager John Gibbons said would make or break their season.
Fans booed after Pierzynski gave Chicago a 5-3 lead in the fifth with his homer off Halladay (13-3).
Halladay -- the 2003 AL Cy Young winner -- lost for the first time since June 18, at Florida -- a span of nine starts. He tied his season high by allowing five runs and 10 hits in six-plus innings.
"It's a tough team. I wasn't able to hold it. It's frustrating, especially with the way things have gone for our guys here," Halladay said. "It came down to one pitch, Pierzynski, and that was the game."
Glaus hit a three-run homer over the center field wall in the first and added a solo shot to right in the ninth.
Thome hit an RBI double in the third and Scott Podsednik had a run-scoring double in the fourth to cut it to 3-2.
Thome doubled in the fifth and Konerko singled before Pierzynski hit his ninth home run.
After Konerko beat out an infield single in the ninth, Jermaine Dye hit an RBI single to make it 6-3.
- Garland is 8-2 in 12 starts against Toronto.
- Halladay threw 30 pitches in the first inning.
- The White Sox have won 15 of their last 24 against the Blue Jays.