Mr Khan has staunchly denied allegations by Sharif's Pakistan Muslim League-Nawaz (PML-N) party that he is getting help from the military, which has ruled Pakistan for about half of its history. Pakistan faces a mounting economic crisis that is likely to require a bailout by the International Monetary Fund, although PTI has not ruled out seeking succour from China, Islamabad's closest ally.
Authorities said on Thursday that the full results would be delayed due to technical failures in an electronic reporting system, and that tallying was now being conducted manually.
Electoral authorities said official results declaring an outright victor were not expected before late Thursday morning.
ECP secretary Babar Yaqoob said Result Transmission Service failed after results of 25,000 out of 85,000 polling stations were uploaded.
As election workers sorted through massive piles of paper ballots, other major parties including the Pakistan Peoples Party (PPP) also alleged the count was being manipulated.
"When an election is believed to be unfree and unfair, knowing that the procedural aspects of the election have been carried out successfully offers little consolation", said Kugelman. "There is no stain".
All parties, aside from the leading PTI are raising allegations of vote fixing, including reports of election monitors being forced out of polling stations.
A party can only form the government if it manages to clinch 172 seats in total.
In NA-53 Islamabad-II constituency, Khan is leading with 7,440 votes over former prime minister Shahid Khaqan Abbasi, who has garnered 3,010 votes.
It was hit by several bombings during the brief but acrimonious election campaign - including a devastating blast claimed by the Islamic State group which killed 153 people this month - Pakistan's deadliest ever suicide attack.
The elections mark only the second time in Pakistan's 70-year history that a civilian government has completed a full term and handed over power to another civilian administration through the ballot box.
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Youthful supporters of Mr Khan, who campaigned relentlessly against political corruption and elitism, sang and danced in cities and towns across the country all evening, celebrating what some called a new day in Pakistani political leadership, free of corruption and dedicated to the public good.
The vote and campaigning have been marred by violence.
Pakistan's cricketer-politician Imran Khan's Pakistan Tehreek-e-Insaf is far ahead of Nawaz Sharif's Pakistan Muslim League-Nawaz in the national elections held yesterday, though it still has some way to go for absolute majority.
A complaint was also received against former president and PPP Co-chairman Asif Ali Zardari for barring people from voting in Badin.
"It is a sheer rigging. However, we condemn the incident of Quetta where people who were electing their future leadership was attacked", he said. "We will fight this injustice and use all options", he said, adding that there has been a "blatant violation" of the mandate.
An elderly Pakistani man shows his inked thumb after casting his vote outside a polling station during general elections in Lahore.
Mr Gahler also visited a polling station and asked a number of questions from presiding officer Muhammad Yousuf, who is a faculty member at the Federal Urdu University.
"This is the warning bell of a serious threat", said PPP senator Sherry Rehman.
The election commission has not released official results yet.
In addition, the election has been plagued by widespread allegations that the army was working behind the scenes to skew the contest in Khan's favor.