The winger, on loan at Everton from Premier League rivals Chelsea, hit home the winner five minutes from time to give Kwesi Appiah's men victory in the Group E clash in Lome.
Having been held to a 1-1 draw by Uganda last Saturday, Ghana appeared set for further disappointment when Floyd Ayite put the hosts ahead after 12 minutes.
First-half goals from Asamoah Gyan and Emmanuel Agyemang-Badu quickly turned things around for Ghana, only for Emmanuel Adebayor to seemingly rescue a point for Togo 13 minutes from time.
But the hosts were left heartbroken as Atsu settled the game in Ghana's favour, boosting their hopes of qualifying for a competition they have won on four occasions.
Togo will have been keen to get back to winning ways after suffering a 2-1 defeat to Guinea in their opening match last Friday.
And Tchakala Tchanile's men promptly made a superb start as Ayite capitalised on a defensive mistake from the visitors to find the net at the second time of asking after seeing his initial effort blocked by goalkeeper Stephen Adams.
Yet Togo's lead lasted just 12 minutes, striker Gyan levelling matters with a towering header into the bottom corner, before midfielder Agyemang-Badu completed the turnaround in the 34th minute.
The Udinese man was left unmarked by the Togo defence and made no mistake as he nodded home Abdul Rahman's low cross at the near post.
Ghana held out for much of the second half with little difficulty, however, Adebayor set the stage for a frantic finale when he netted with a towering header.
But it was Atsu who had the final say, the 22-year-old using his pace to break free from the defence, confidently slotting home to seal all three points for Ghana.