Champions League winners Liverpool's total pipped that of semifinalists Ajax, who had five players including coveted defender Matthijs de Ligt named in the 20-player squad.
A panel of nine experts including England manager Gareth Southgate, Belgium coach Roberto Martinez and former Manchester United manager David Moyes picked the squad, which included both Barcelona's Lionel Messi and Cristiano Ronaldo of Juventus.
Messi finished as outright top scorer in the tournament, with 12 goals, for the first time since the 2011-12 campaign, taking the crown from Ronaldo, who ended his European campaign with six strikes.
Champions League Squad of the Season:
Goalkeepers: Alisson (Liverpool), Marc-Andre ter Stegen (Barcelona)
Defenders: Virgil van Dijk (Liverpool) Matthijs de Ligt (Ajax) Jan Vertonghen (Tottenham) Trent Alexander-Arnold (Liverpool) Andrew Robertson (Liverpool)
Midfielders: Moussa Sissoko (Tottenham) Hakim Ziyech (Ajax) Kevin De Bruyne (Manchester City) Frenkie de Jong (Ajax) Tanguy Ndombele (Lyon) Georginio Wijnaldum (Liverpool) David Neres (Ajax) Raheem Sterling (Manchester City)
Forwards: Lionel Messi (Barcelona) Dusan Tadic (Ajax) Sadio Mane (Liverpool) Cristiano Ronaldo (Juventus) Lucas Moura (Tottenham)