Barton's sharply hit grounder bounced off Jose Altuve's glove and into right field to send two home. Rookie George Springer's error on that play allowed a third run to score, sending the few fans left filing to the exits.
Donaldson, who homered twice on Thursday night, connected again on Friday with a shot off Anthony Bass to the Crawford Boxes in left field to make it 12-5.
Jed Lowrie had two hits and two RBIs to help the A's improve to 5-0 against Houston this season and 25-5 against the Astros all-time.
Altuve had three hits and drove in a run for Houston, which has lost 10 of its last 12 games and allowed 22 runs in the first two games of this four-game series.
Former Astro Fernando Abad hit Jason Castro on the backside with a pitch with one out in the ninth inning. Castro jawed with catcher Derek Norris before heading to first base. Houston manager Bo Porter darted out of the dugout and began yelling at plate umpire Jordan Baker and was ejected.
Castro's plunking came after Lowrie accused Houston of intentionally hitting him with a pitch Thursday night for an incident in the last series between these teams when the Astros were miffed after he attempted a bunt with a seven-run lead in the first inning.
The A's put up four runs in the second inning and extended the lead to 5-1 in the fourth. Houston answered with four runs in the bottom of the inning to tie it up.
Jesse Chavez had his first tough outing of the season, allowing a career-high eight hits with five runs - four earned - in five innings. He entered having allowed just one earned run in each of his four starts and had a 1.38 ERA.
Houston starter Brad Peacock yielded five hits and five runs, including three earned, with a career-most six walks in five innings.
A's left fielder Yoenis Cespedes sat out Friday after straining his left hamstring a night before. Manager Bob Melvin said he expects him to be out a couple of days. ... Houston right-handed reliever Jesse Crain, who has been on the disabled list all season after biceps surgery during spring training has been shut down after developing bursitis in his shoulder. General manager Jeff Luhnow said the current problem is not related to his surgery. He was scheduled to return in early May, but Luhnow said he will not be ready then and he should have a updated timetable for his return in about 10 days. ... RHP Mark Appel, the first overall pick by the Astros in 2013, has been sent to extended spring training after starting the season at Single-A Lancaster. Luhnow said he is not injured but was behind after missing most of spring training after an emergency appendectomy and needed more games to get ''more used to the pro routine.''