Johnny Cueto struck out nine in seven strong innings in the 2-1 win.
Cueto (8-5) allowed only three hits and two walks -- most of which came in the fifth inning, when he escaped a bases-loaded situation.
The right-hander lowered his earned run average to 1.94, which leads the National League, and picked up the win after the Cincinnati bullpen managed to hang on to the lead.
Baker is 300-304 in four seasons with the Reds, including a National League Central title in 2010.
Right-hander Bronson Arroyo starts for Cincinnati against the Padres and aims for his first win since June 25. The Key West, Fla. native improved to 7-6 on the season with a 10-5 win at Baltimore, but is 0-3 in seven starts since and his earned run average has swelled from 5.01 to 5.48.
He's given up four runs or more in six of those seven starts.
Arroyo is 4-7 lifetime against the Padres in 12 starts.
Luis Martinez added an RBI single for the Padres, who salvaged a split of the four-game series.
San Diego starter Cory Luebke gave up two runs on three hits with four walks and eight strikeouts in five innings. Four relievers held the Mets hitless over the final four frames.
Tonight, right-hander Mat Latos gets the call against the Reds and looks to get a step closer to a second straight double-digit win season. The 23-year- old was 14-10 for the Padres over 31 starts last year after debuting in 2009 with four wins in 10 starts.
He's split two career meetings with the Reds while allowing four runs on five hits in 13 innings.
In his last outing, on Aug. 7, Latos gave up two runs in seven innings of a 7-3 defeat of Pittsburgh.
Cincinnati took two of three from the Padres earlier in the year.