Haller came off the bench at the start of the second half and netted goals in the 54th and 69th minutes as Ajax overturned a half-time deficit to keep up their 100% run in the group.
But Ajax did not take long to impose their supremacy and equalised after a long pass out of defence from Lisandro Martinez set Nicolas Tagliafico away down the left wing and his square ball provided an easy conversion for Haller.
Ajax's winner came from Dusan Tadic's free kick, initially falling to Martinez who miss-hit his shot but Haller stuck out a lanky leg to steer the ball home.
Haller had the ball in the net in stoppage time but his teammate David Neres was offside to deny him a hat trick.
Ajax, who rested several regulars in Wednesday's game, can complete a full house of wins when they conclude the group campaign at home to Portuguese side Sporting on Dec. 7.