It was Kruse's third goal in four games for Bochum with the win ending a run of two straight defeats for the German second division club.
Bochum took the lead in the 24th minute thanks to a powerful drive from striker Kevin Stoger from just inside the penalty area.
Kruse found the net only minutes later when he received the ball in the box unmarked before curling around the advancing goalkeeper.
A late flurry from Ingolstadt had Bochum on the back foot in the dying stages of the clash, but Kruse's side manged to cling on for a morale boosting win.
Socceroos teammate Jamie Maclaren also featured in 2. Bundesliga action overnight as club side SV Darmstadt 98 made a dramatic comeback to secure a 3-3 draw with Dynamo Dresden.
Maclaren came off the bench in the 72nd minute as Darmstadt scored two added time goals to snatch a point at the death.
