"That was the only option we had," the Atlanta Braves manager said.
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Hinske had three hits, including a tie-breaking single in the seventh, Mather had a two-run single and the Braves used a makeshift lineup to beat Houston 3-2 on Monday night.
Gonzalez subbed Hinske in left field and Mather in right as the Braves were missing third baseman Chipper Jones and right fielder Jason Heyward from their starting lineup.
"We're just trying to fill in for the guys who are down right now," Hinske said.
Heyward, who missed his sixth straight start with inflammation in his right shoulder, entered the game in the eighth inning as a defensive replacement. In his first at-bat since Tuesday, Heyward hit a grounder in the eighth and was safe on shortstop Clint Barmes' throwing error.
Gonzalez said Heyward will start Tuesday's finale of the two-game series.
An MRI on Sunday revealed Jones has a small meniscus tear in his right knee. He had two shots in the knee Sunday and said he felt better on Monday.
Jones said he may start Tuesday if he continues to improve. If there is persistent pain, however, Jones could need arthroscopic surgery.
Tommy Hanson (5-3) gave up three hits and two runs, one earned, in seven innings. He struck out 10, one shy of his career high, with only one walk.
Hanson, who lowered his ERA to 2.35, has won his last four decisions. He said he wanted to help make sure the Braves avoided a letdown after winning two of three games against first-place Philadelphia.
"I think the biggest thing was we got a little bit of momentum this weekend against Philly and just wanted to keep rolling," Hanson said.
Craig Kimbrel gave up a single to Carlos Lee but struck out the side in the ninth for his 11th save.
Hanson struggled only against Matt Downs, who had a homer and RBI double.
"He's got good stuff," Downs said of Hanson. "He's got great stuff. I just got a couple balls up in the zone and put some good wood on it."
After Fernando Abad (1-4) walked Nate McLouth and Dan Uggla in the seventh, Hinske's single to right drove in McLouth for a 3-2 lead.
Downs hit a homer into the chilly wind blowing in from left field to give Houston a 1-0 lead in the fifth. Following Mather's two-run single for Atlanta in the sixth, Downs' double in the seventh drove in Lee, who reached on third baseman Martin Prado's throwing error, for a 2-2 tie.
Houston's Brett Myers lasted six innings despite needing 56 pitches to escape bases-loaded jams in each of the first two innings. The right-hander gave up eight hits and two runs with six strikeouts and three walks.
"I was trying to throw strikes," Myers said. "I was trying to get out of jams. I was trying to do damage control."
Prado, the regular in left field, filled in for Jones at third base and had the defensive play of the game in the first when he made a diving stop of a sharp grounder hit by Lee. Prado's throw from his knees beat Lee to first base.
Prado made another strong play in the third, charging in to field Michael Bourn's bunt and throwing out the speedy runner. He threw high to first for an error after fielding another grounder from Lee in the seventh.
Prado was primarily a second baseman before moving to the outfield after the Braves made an offseason trade for Uggla.
Lee's fourth-inning single gave him a 10-game hitting streak. He is hitting .400 (16 for 40) with two homers in the streak. ... Gonzalez said RHP Julio Teheran will be recalled from Triple-A Gwinnett to start on Wednesday at Arizona. ... Prado had a first-inning single before he hit into three double plays.