O'Neal started the second half in the locker room because of shortness of breath. He returned with 5:29 left in the third quarter.
Harrington said he knew he had to step up in O'Neal's absence.
"I didn't know if he was going to come back or not, so I just wanted to become a post presence,'' Harrington said.
O'Neal said the doctors told him he was OK.
"I couldn't really breath,'' O'Neal said. "I started to get woozy. I just wanted to make sure that I wasn't going to fall down and die. They have really good doctors here, but knowing me it is their doctors and they are losing. They kept me back there a long time. The whole time I was kind of rushing and saying, 'Who is winning?' They said I was fine.''
"They checked me after the game. My blood pressure is a little high. Hopefully, it's not anything serious with my chest.''
Harrington scored six straight points to give the Pacers an 88-85 lead with 5:04 remaining.
Morris Peterson tied it for Toronto with two free throws with 1:41 left, but Jamaal Tinsley made one of two free throws to give Indiana the lead.
Williams later stole a pass from Tinsley with 19 seconds left, but Antonio Davis missed a 12-foot jumper with 4 seconds remaining. Ron Artest grabbed the rebound, was fouled and made two free throws to give Indiana a 97-94 lead with 2.8 seconds left.
"Antonio had a great look,'' Toronto coach Lenny Wilkens said. "I'll take that every time.''
The Pacers then intentionally fouled Peterson, who made his first throw before the Raptors committed a lane violation to seal the victory for the Pacers.
"I thought we deserved to win,'' Peterson said. "This is definitely a building block for us. We can compete with the guys we have.''
The Raptors, who had just nine players in uniform, signed guard Jermaine Jackson earlier in the day after being granted their second roster exemption this month by the NBA under a special hardship rule.
Vince Carter, sidelined with a strained left quadriceps tendon, isn't expected back for at least a week.
Lenard had 16 points and Peterson had 12 as Toronto led 56-49 at
The Pacers outrebounded the Raptors 51-40. ... Indiana's
bench outscored Toronto's 31-5. ... Indiana coach Isiah Thomas
resigned as general manager of the Raptors five years to the date.
The crowd booed him before the game. Thomas won his first game in
Toronto as Indiana's coach ... Davis had 19 points and 10 rebounds,
and had four of Toronto's eight blocks in the first half.