The veteran politician, who was first elected as a regional MSP for Glasgow in 2003, had hoped to win the Kelvin seat following the retirement of the SNP’s Sandra White.
But even with hours of the count yet to go, Mr Harvie told The Scotsman he expected the SNP’s Kaukab Stewart to be elected.
“It looks like we’re probably going to get a solid result, but the SNP had a good day as well, so I wouldn’t be predicting the seat is going to flip,” he said.
“I think we’ve seen movement in the right direction, especially in the regional list results, including in Kelvin.
“But I think a lack of canvassing, and the lack of students able to be in the constituency, has had an impact. I think everyone is expecting Kaukab to be elected.”
Five years ago, Ms White secured a comfortable 4,048 majority.
Mr Harvie came second with 6,916 votes – nearly 1,000 more than Scottish Labour, and more than double that of the Tories. This time around, the SNP look set to repeat its 2016 clean sweep of Glasgow.
With the Greens’ Alison Johnstone seeing her vote share fall on Friday in Edinburgh Central – won by the SNP’s Angus Robertson – the party’s hopes of success from one of its 12 constituency candidates are looking increasingly faint.
However, Mr Harvie expressed optimism that it would fare better on the regional lists, where he is the party’s top candidate for Glasgow.
The Greens hope to return even more than the record seven MSPS it secured in 2003, with some polls in the run up to the vote suggesting it could return a double-digit parliamentary group at Holyrood.
“I think where we are at the moment, we might be somewhere between the top end of what some of the polls predicted for the lists, and the lower predictions in some lower polls,” Mr Harvie said. “I expect that we might end up somewhere in the middle.
"The tricky thing is the difference between getting our first seat on the board in places like the South of Scotland, it could be a very marginal difference."