Ally Schlegel scored a brace to lift the Nittany Lions to victory in the back-and-forth match.
Zoe Weatherington put on a fierce showing in the sweep against Rutgers on Sunday afternoon.
Penn State wasn't able to score in even strength and split the series against its CHA rivals.
The Nittany Lions scored three goals in about four minutes to tie the game late in the third period.
Liam Souliere recorded his second consecutive shutout.
Unable to overcome Indiana's first half goal, Penn State fell out of the Big Ten Tournament in the quarterfinal match.