Morata made a brilliant impact off the bench as the Blues suffered a 3-2 loss against Burnley on the opening day of the new season, scoring one and setting up David Luiz for the other.
And the Spaniard has been preferred to Michy Batshuayi for Chelsea's visit to Wembley Stadium, with the Belgium international dropping to the bench as a result.
There is also a first start for Bakayoko following his summer move from Monaco, with Andreas Christensen replacing Gary Cahill, who misses out through suspension.
Tottenham, on the flip side, welcome back Kieran Trippier after the defender was absent during his side's 2-0 victory over Newcastle United on the opening weekend.
Victor Wanyama, who was on the bench at Newcastle, returns to the starting line up for Mauricio Pochettino's men as they look to make it two league wins from two in 2017-18.
Tottenham XI: Lloris; Trippier, Alderweireld, Vertonghen, Davies; Dier, Wanyama, Dembele; Alli, Eriksen; Kane.
Subs: Vorm, Walker-Peters, Wimmer, Winks, Sissoko, Son, Janssen.
Chelsea XI: Courtois; Christensen, David Luiz, Rudiger; Azpilicueta, Kante, Bakayoko, Alonso; Moses, Morata, Willian.
Subs: Caballero, Musonda, Kenedy, Pedro, Batshuayi, Tomori, Scott.