While Mayor Ford applauded, he didn't stand up during the moment of recognition of the city's recent WorldPride festival, a celebration of LGBT rights.
This raised further questions about whether the mayor is homophobic.
"You guys have asked me this question for 14 years," responded Ford after the council session. "I'm not homophobic."
Ford was previously accused of being anti-gay when he was recorded using homophobic language. He also has not attended any Pride parades during his tenure as mayor and city councillor.
"As council and city staff stand to congratulate Toronto's WorldPride organizers, Rob Ford remains sitting and silent," Coun. Josh Matlow tweeted, along with a photo of the moment.
Coun. Mike Layton tweeted that Ford's behaviour was "disgraceful."
Ford did not appear to clap further as Kelly then singled out specific individuals for recognition.
The applause was a response to Deputy Mayor Norm Kelly calling on his fellow councillors to recognize the organizers, volunteers and organizations that helped make WorldPride and its events a success.
"I would invite you to join me in thanking all of these people and institutions for their contribution to our city," Kelly said.
The mayor did not stand up at this moment, though he turned and clapped.
The mayor was in recently rehab for about two months for substance abuse. He returned to Toronto the day after WorldPride ended.
When Ford came back, he issued a statement that included an apology "to everyone who was hurt by my words and my actions."
Well ahead of this year's parade and before he decided to head to rehab, the mayor had indicated he would not be attending the Pride parade.