The two parties had been engaged in talks since Sunday, but these deadlocked, which made the strike action more imminent.
But the two parties agreed to meet on Monday for talks that lasted for more than four hours.
Last night, Nehawu general secretary Zola Saphetha confirmed that the two parties reached a settlement agreement.
He said his union had managed to push the IEC to implement the new pay organogram by September 1.
The union said that three years ago, a recommendation was made by a service provider to the IEC to change the salary bands and structure of its employees with immediate effect, but the IEC allegedly failed to do so.
Sapheta also said the two parties have agreed to have a relook at the suggestions that the same employees should be given access to transport and benefits while performing their electoral duties.
“In implementing the resolutions reached, a committee of six has been established to ensure the implementation of the agreements.
"As Nehawu, we remain committed to ensuring that we fight for better wages and improved working conditions for our members,” Saphetha said.
The dispute overshadowed reports of the discovery of folded ballot papers found on the streets of Tzaneen in Limpopo.
Various high-profile people, including Archbishop Emeritus Desmond Tutu, were among the first who cast their special votes on Monday.
Tutu voted at his Milnerton home in Cape Town on Monday.
Some ANC heavyweights, such as International Relations Minister Lindiwe Sisulu, who voted at Linden High School in Joburg, said she applied for a special vote as her party had deployed her to KwaZulu-Natal to monitor elections there.
Outside the voting station, she said: “This is where I voted since 1994. I would always bring my mother (Albertina Sisulu) to the same station to cast our votes," the minister said.
In Pretoria, house number 67 on Maunde Street in Atteridgeville was a centre of attraction as one of the oldest voters in South Africa, Mmaphuthi Mabitsela, 107, made her X.
Mabitsela said she voted because she wanted the government to help out with her utility bills and job creation for the youth.
Mabitsela was ecstatic to show the blue ink on her left thumb - the indelible mark that she participated in the elections.
“I am very happy for voting for the party of my choice,” the beaming gogo said.
In Mamelodi, other elderly people expressed excitement as they took part in the two-day special voting.
Octogenarian Rosinah Mabokela also voted. She said she was not going to make it to a polling station because of arthritis, which affected her walking ability.
“I was worried that I might not make it to the voting station on May 8, but I am happy that I have voted."
She said that she would continue to vote for as long as she was still alive.
“I started voting during the times of Mandela.
"I am going to continue voting should God continue to grant me more days of life,” Mabokela said.
Maria Makate, 78, who is partially blind, hoped her vote would make a difference in her community.
“Nowadays there is too much unemployment. Our children are not working and I have to take care of them with my social grant,” Makate said.
The special votes continue on Tuesday.