Prof Michael Arthur said that he "regretted" the personal difficulty suffered by Sir Tim, who has been accused of sexism.
But he said his comments about women in laboratories had struck "such a discordant note".
He said they were at odds with the university's aim to create a working environment where women felt supported.
Prof Arthur added in a statement in the staff news section of the UCL website that Sir Tim's offer of resignation was his personal choice and the honourable thing to do.
He said that despite many calls for him to reinstate Sir Tim, there had been "very significant" representations to him not to do so - and not only from women in science.
"Our view is that reversing that decision would send entirely the wrong signal and I have reason to believe that Sir Tim would also not want that to happen," he said.
The Nobel prize-winning scientist resigned from his honorary post at UCL earlier this month following the reaction to comments he made at a science journalism conference in South Korea.
He said at a lunch that women in labs "cry" when criticised and "fall in love" with male counterparts.
His resignation prompted many messages of support for Sir Tim from scientists, including many Nobel prize winners calling for his reinstatement. His supporters said that his comments were meant as a self deprecating satirical joke and were taken out of context.
The evolutionary biologist and author, Prof Richard Dawkins, described criticism of Sir Tim as a "witch-hunt"
But Prof Arthur said in his statement  that "an honorary appointment is meant to bring honour both to the person and to the university".
"Sir Tim has apologised for his remarks, and in no way do they diminish his reputation as a scientist.
"However, they do contradict the basic values of UCL - even if meant to be taken lightly - and because of that I believe we were right to accept his resignation.
"Our commitment to gender equality and our support for women in science was and is the ultimate concern."
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The Premiership winner tied the knot with Rebekah Nicholson at Peckforton Castle in Cheshire.
Guests included stars from the worlds of music and football.
The 29-year-old had already postponed the big day three times to avoid footballing commitments but will miss England's friendly on Friday.
Fellow England internationals were all apparently invited but manager Roy Hodgson poured cold water on the plans.
But he did give permission to the Foxes' Danny Drinkwater - as long as he made it to England training by 17:00.
With England commitments taking up much of the summer, Vardy - who signed from then non-league Fleetwood Town four years ago - has said he will delay his honeymoon.
Guests at the glitzy bash included One Direction singer Louis Tomlinson and Kasabian guitarist - and Foxes fan - Sergio Pizzorno.
Vardy's Premier League-winning team-mates Wes Morgan, Danny Simpson and Marcin Wasilewski also saw him tie the knot along with best man David Nugent.
Vardy has previously said it would be a quiet night for him as he prepares for a busy summer of football.

30 December 2015 Last updated at 13:37 GMT
The storm has also brought heavy rain and gales to Northern Ireland and Scotland, with flood warnings in place across the UK.
Hundreds of homes have been evacuated and thousands left without power with many areas fearing the storm will bring more flooding.
The president of University College London has said that Prof Sir Tim Hunt will not be reinstated.
[NEXT_CONCEPT]
Leicester City striker Jamie Vardy has got married at a star-studded ceremony - after postponing his nuptials three times.
[NEXT_CONCEPT]
A large batch of sea foam has washed up on the coastal town of Tramore as Storm Frank moved across the Republic of Ireland.