The military rejected the accusations and said it has no "direct role" in the electoral process.
The stock market shot up almost 2 percent in early trading on relief the likely coalition government will not be a weak one. The results had been due by 2am (2100 GMT).
But Yaqoob said the vote-counting system, which he said was untested, had "crashed", adding: "There is definitely no conspiracy, no one wants to influence the results".
The PML-N leader is contesting the election from NA-129 in Lahore.
The Pakistan Muslim League-Nawaz (PML-N), the party of jailed ex-prime minister Nawaz Sharif, has called the count an "assault on democracy" in a country which has a history of military rule. Nawaz Sharif was ousted from power past year and jailed over a corruption conviction days before the vote, removing Khan's most risky rival.
In Islamabad, PTI bagged all seats, where in NA-54 (Islamabad-III), Asad Umer defeated Anjum Aqeel Khan, while in NA-53 (Islamabad II) Imran Khan defeated former Abbasi.
If Khan's lead holds, his party will likely be able to form a government with smaller parties and independents, avoiding the prospect of weeks of haggling.
Mr Khan told ITV News that he believes this election is "one of the freest and fairest" the country has seen. "Prime Minister Imran Khan", although his party has yet to officially declare victory.
While over 12,500 candidates of over 100 parties are contesting for 849 seats of National Assembly four provincial assemblies, the main contest is between Pakistan Muslim League-Nawaz (PML-N) President Shehbaz Sharif, Pakistan People's Party (PPP) Chairman Bilawal Bhutto Zardari and Pakistan Tehreek-e-Insaf (PTI) chief Imran Khan.
At least 28 people were killed and 35 wounded in a suicide attack on a polling station in the southwestern Pakistani city of Quetta, officials said, as millions voted in a nationwide election Wednesday.
Khan, 65, campaigned on populist promises to build a "New Pakistan" and vowed to eradicate corruption, clean up the environment and construct an "Islamic welfare" state.
Many experts contend that it will be business as usual whoever wins the election, with the military - which has ruled the country directly or indirectly for much of its 71-year history - remaining Pakistan's de facto ruler.
The vote and campaigning have been marred by violence. Preliminary results, however, indicated that Pakistan Tehreek-i-Insaf (PTI) had obtained a clear edge over other parties as results trickled in, giving pockets of supporters reason to celebrate in parts of the country, media reports said.
"It is a sheer rigging".
"Imran Khan doesn't have many friends or allies; he's not someone who really knows how to work with people", said Mohammad Malick, a popular political talk show host, referring to Khan's famous stubbornness.
"I think you could have a complete collapse in terms of ability to form a government right after the election", said Moeed Yusuf, a Pakistani analyst at the United States Institute of Peace, a Washington think tank.
Jeff M. Smith - from the Heritage Foundation - said it was important to acknowledge that a peaceful transition of power via a democratic election is still a rare commodity in Pakistan and thus would be a positive step forward.
Sharif's PML-N has condemned the legal cases facing its members, and reported pressures to leave the party along with harassment to prevent it from returning to power after its absolute majority in 2013. The army has dismissed these allegations. It's an incredible lesson in tenacity, belief & refusal to accept defeat.