Less than a week after scoring five second-half goals in a 6-1 thrashing of Poland, Roberto Martinez's side was without several star names including Thibaut Courtois, Kevin De Bruyne and Romelu Lukaku for the return fixture.
But Belgium was mostly comfortable after Batshuayi nodded it into an early lead, with Nicola Zalewski and Karol Swiderski squandering Poland's best chances to equalise.
Martinez's team trails Netherlands by three points with two group-stage contests remaining, meaning the two rivals could be set for a straight shoot-out for qualification when they meet in September.
Wojciech Szczesny raced off his line to deny Thorgan Hazard early on, but he was helpless when Batshuayi headed Belgium into a 16th-minute lead, the Chelsea man stooping to divert Youri Tielemans' cross into bottom-right corner.
Sebastian Szymanski sent a wild volley over from a good position after half an hour, before Eden Hazard was flagged offside having beaten Szczesny with a deft chip after racing onto Batshuayi's pass.
Although Belgium dominated much of the opening period, Zalewski went agonisingly close to levelling shortly before the break when he volleyed Robert Lewandowski's right-wing cross narrowly wide.
Thorgan Hazard almost doubled Belgium's lead when he sent a low strike wide of the left-hand post after 52 minutes, before Jan Vertonghen saw a driven cross deflected just wide of the bottom-left corner.
Swiderski twice went close to a dramatic equaliser when he forced Simon Mignolet into an acrobatic save before clipping the post with a deft header, but Belgium held on for its second Nations League win of the campaign.