Dr Kermit Gosnell, 72, was acquitted on another charge of killing a fourth baby, who let out a whimper before he cut its neck, prosecutors said.
He was also found guilty of involuntary manslaughter of an adult patient who died of an overdose.
The case was seized on by both sides in the US debate over abortion.
Prosecutors are seeking the death penalty for Gosnell.
He performed thousands of abortions over a career spanning three decades. Officials said his medical practice earned him about $1.8m (£1.1m) a year.
'House of horrors'
Former staff members of the clinic testified that he had routinely performed illegal late-term abortions past Pennsylvania's 24-week limit.
The trial heard how Gosnell would deliver babies alive then use scissors to "snip" - as he referred to it - their spines.
Among the untrained staff who helped to perform the terminations was Gosnell's wife, Pearl. She pleaded guilty to a number of charges and testified against him.
The trial heard that one of the babies was almost 30 weeks when aborted, and had grown so large that Gosnell joked it could "walk to the bus". A second foetus was said to have clung to life for about 20 minutes.
A third was born in a toilet and seen moving before a clinic employee severed its spinal cord, according to testimony.
Gosnell's lawyer, Jack McMahon, had argued that none of the foetuses was born alive. Any movement was posthumous twitching or spasms, he said.
Defence lawyers for Kermit Gosnell said he was targeted because of his race
The attorney branded prosecutors "racist" for pursuing his client, who is black. Gosnell did not testify and no witnesses were called in his defence.
Prosecutors said Gosnell had run a filthy "house of horrors" with unqualified staff - including those who administered a lethal dose of sedatives to Karnamaya Mongar, a 41-year-old refugee from Nepal.
Defence lawyers had argued the abortion patient's 2009 death was a result of unforeseen complications.
Prosecutor Ed Cameron said to Gosnell during closing arguments: "Are you human? To med these women up and stick knives in the backs of babies?"
"He created an assembly line with no regard for these women whatsoever," Mr Cameron had said.
Severed feet
Officials said a raid of the clinic, in a poor section of West Philadelphia, had turned up bags and bottles of foetal remains, including severed feet.
The clinic also had bloodstained furniture, dirty medical tools and cats roaming the premises.
Karnamaya Mongar (left) died of a sedative overdose at the clinic
During the trial, Judge Jeffrey Minehart threw out three other murder charges involving aborted foetuses.
The jury was earlier deadlocked on two counts against Gosnell, but did not specify which of the multiple counts.
After the verdict was read on Monday, Gosnell appeared calm, the Associated Press news agency reports.
The jury will return next week to hear evidence on whether he should face the death penalty.
The trial became a cudgel for those on both sides of the US abortion debate.
Anti-abortion activists said the case exposed the grim reality of the procedure, and accused media of ignoring the case because of liberal bias.
But abortion rights groups warned it showed what would happen if laws on such procedures were tightened, driving desperate women to unregulated backstreet clinics.
The case also exposed failings by Pennsylvania's health authorities.
Officials had failed to conduct routine inspections of all of its abortion clinics for 15 years by the time Gosnell's operation was raided and closed more than two years ago.
Two top state health department officials were sacked, and Pennsylvania imposed tougher rules for clinics.
Bbc.co.uk
