Modric won the award ahead of Cristiano Ronaldo and Mohamed Salah.
"Congrats Mohamed Salah on your seventh best goal from last season winning goal of the year #baller #topbin #oneofmanyworldies", Milner tweeted.
Best Women's Player appropriately went to Brazil's Marta, who is probably the sport's greatest current proponent, whilst Best Men's Coach went to French national team coach Didier Deschamps, and Reynald Pedros won the Best Women's Coach award for Olympique Lyonnais.
Liverpool's Salah returned to the Premier League with mixed expectations, following a two-year stint with Roma and bumpy spell at Chelsea, only to score a Premier League record 32 goals, and 44 in total last season.
Salah's teammate James Milner spoke for several fans with his take on the award.
Receiving a pass from right back Joe Gomez, Salah shrugged off Cuca Martina, twisted inside Idrissa Gueye, and curled a left-footed shot around Ashley Williams and into the top corner.
"I would like to thank those who voted for me".
In Modric's acceptance speech he paid tribute to his hero Zvonimir Boban, captain of the 1998 Croatian side who excelled in France to finish third in the World Cup.
Meanwhile, Modric led Croatia to the final and collected the Golden Ball award.
"Without my coaches, I would not have won this and without my family I would not be the player I am today", said 33-year-old Modric.
The best goalkeeper award will be fought for between Thibaut Courtois, Kasper Schmeichel and Hugo Lloris.
Pele sent his good wishes, tweeting: "Congratulations to Luka and Marta on winning the #TheBest awards tonight".