Prime Minister Anthony Albanese led the tributes to Dr Haines a week after the member for Indi was struck repeatedly by a four-wheel drive in an allegedly deliberate attack outside her office in Wangaratta, northern Victoria, on October 19.
Dr Haines had both her legs amputated but is now in a stable condition.
It was quieter than a usual sitting day on Monday as MPs, most of whom were wearing white blazers with sprigs of baby's breath flower, filed into the chamber.
Dr Haines' husband, Phil, watched on as details of the alleged attack on this wife were read out by the prime minister.
Mr Haines sat resolute in the gallery, looking up at the ceiling teary-eyed when his wife's good qualities were spoken of.
"The shock from what happened last Monday is like a stone in our hearts," Mr Albanese said, expressing his love, and the love of the nation, was with Dr Haines, her husband, and her family.
"It is hard to think of anyone in this place with a more irrepressible twinkle in the eye, a twinkle that more than hints at a real inner strength."
Orange heart pins, representing the colour Dr Haines uses for her campaigning, held the white flowers in place. Independent MPs embraced as they walked in.
The silhouette of a cockatoo, cut from orange card, was placed on Dr Haines' chair by good friend and colleague Zali Stegall.
Mr Albanese also paid tribute to the bystanders, witnesses, and medical staff who assisted Dr Haines immediately after the alleged attack.
"We are also uplifted in the knowledge that on that terrible afternoon, we saw examples of the best of the Australian character," he said.
A "rising tide of rage" was distorting public discourse, Mr Albanese said, with the normalisation of "the language of grievance and violence".
Fellow crossbenchers Ms Steggall and Monique Ryan both became emotional when speaking about their friend.
''You're the matriarch of the crossbench, always the voice for respectful political debate,'' Ms Steggall said, praising Mr Haines' ''calm resolve and love'' for his wife as a ''balm'' for the nation.
Dr Ryan described the Indi MP as ''a woman of luminous generosity and kindness'' who could put anyone at ease.
Opposition Leader Angus Taylor said it would be a ''resounding moment'' for Australia's democracy should Dr Haines resume her seat in parliament.
''What we must do is call out and confront the actual sources of intolerance, of intimidation, of political violence in our country.''
House of Representatives speaker Milton Dick said Dr Haines treated everyone with respect, ''regardless of title or position".
"I could always count on Helen when I had a particularly difficult day, or if I needed a bit of extra encouragement,'' he said.
Above and to the sides of the chamber, dozens of senators, who had suspended government inquiries to attend, watched on.
Aside from Question Time, Monday's sitting will be devoted to tributes to the Indi MP.
Independent MP Kate Chaney, wearing an orange blazer and a cockatoo brooch in support of Dr Haines, urged other politicians to act with kindness.
"(The pledge) is a very simple thing. It just says: in my political life, I pledge to act with honesty, respect and compassion," she said on ABC Radio.
Dr Haines was the first MP to sign the Compassion in Politics Australia pledge.
Dr Haines was the only independent MP to have all her commitments costed at the last two federal elections, Parliamentary Budget Office representatives revealed at Senate hearings on Monday.
"We recognise that Dr Haines played an important role in parliamentary accountability and transparency," the office's head Sam Reinhardt said.
Parliament opened on Monday with increased security in public areas, which the Australian Federal Police and government are continuing to work on.
A fundraiser for charity Save the Children, set up on Wednesday by Dr Haines' family in lieu of flowers, had surpassed $1.2 million in donations by Sunday afternoon.
