Toby and Jan played the full game at the back, while Mousa came on at half-time.
Belgium, who also beat San Marino by nine goals (10-1) in a 2002 World Cup qualifier, are now six points clear at the top of Group H, having scored 33 goals and conceded just twice.
Elsewhere, Hugo Lloris captained France and kept a clean sheet in a 4-0 home win over Vincent Janssen's Netherlands. Vincent played 64 minutes before being withdrawn. France are top of Group A, with the Netherlands in fourth.
New signing Davinson Sanchez was on the bench for Colombia as they battled out a goalless draw away to Venezuela.