Premier League leaders Spurs lost the reverse fixture 1-0 in October - their only group defeat - and needed a win in front of their 2,000 fans to usurp Antwerp, who had also already booked a last-32 spot.
The visitor more than held its own in a first half devoid of any real action but Vinicius tapped in with 56 minutes played after Gareth Bale's sublime free-kick hit the post and landed at the Brazilian forward's feet.
Son Heung-min and Harry Kane were introduced at that point and the latter played in Lo Celso for the second to ensure Tottenham will be among the seeded sides for Monday's draw.
Alireza Beiranvand kept out long-range efforts from Vinicius and Lo Celso, either side of Cristian Benavente's angled shot being blocked by Davinson Sanchez.
Visiting keeper Beiranvand was called into action again late in a balanced first half as he closed the angle to deny Vinicius after the forward was played in by Lucas Moura.
But the half-time introduction of Steven Bergwijn for Sergio Reguilon and a switch to a four-man defence gave Tottenham more control and they were soon in front.
Bale's dipping free-kick from more than 30 yards out was pushed onto the post by Beiranvand and Vinicius reacted quickest to the loose ball.
Substitutes Son and Kane went close to doubling Tottenham's tally but there was to be no denying Lo Celso, who took Kane's pass in his stride and calmly picked out the bottom-left corner with an outside-of-the-boot finish.
That was the 27th goal Kane has been directly involved in for Tottenham this season - more than he recorded in 34 games in 2019-2020 - and he would have added another goal to his collection had he not slipped when shooting late on.