Orient believed there was only minimal contact, if any, when Ward went down under sub Brian Saah's innocuous challenge on the hour.
It could hardly be a more touchy subject, because new Torquay chairman Chris Roberts recently introduced a highly controversial anti-cheating initiative which could end with him sacking a player found guilty three times.
Saah had only been on the pitch three minutes, but after referee Iain Williamson's decision, he had to watch Ward pick himself up and drill the penalty past O's keeper Glyn Garner for his eighth goal of the season.
"I was a long way away, but Brian tells me he didn't touch Ward, and people who were in a much better position agree with him," said Orient boss Martin Ling.
"The linesman had a better view and he didn't make a signal. But the referee, who was behind the play, gives it. It looked a very poor decision."
In fairness, League Two Torquay deserved their lead.
Orient couldn't cope with the combination of Ward's pace and former O's striker Lee Thorpe's flicks and only Garner and the alert Alton Thelwell kept the Gulls at bay well into the second half.
Garner saved well from Ward twice, Thorpe and Mat Hockley before their breakthrough.
But the goal fired Orient and, with Ling sending on strikers Paul Connor and on-loan Charlton starlet James Walker, they hit back hard.
They equalised in the 76th minute when right-winger Shane Tudor picked out left-winger Wayne Corden with a raking crossfield pass and Corden cut in to beat Nathan Abbey from 15 yards.
Three times in the last ten minutes Connor nearly snatched the winner, heading the best chance wide from a Matt Lockwood cross.
Ling added: "We didn't play at all for an hour, so I'm quite pleased to come away with a replay.
"But we're facing midweek games for five weeks on the trot now, so I don't think we'll be doing too much training."
New Torquay manager Lubos Kubik, the former Czech international defender, speaks only broken English, but he said: "I have only worked with the players for five days and I have tried to push up their confidence.
"I thought we showed good quality in defence.
"But I am unhappy because we have to go next week to London to play again, and it will be hard for us there."