Downes was subbed at half-time of Southampton’s dramatic 2-1 win over Swansea after seeing yellow in the first half.
The 27 year old forced Melker Widell to the ground after fouling former teammate Liam Cullen, earning him a yellow card.
Eckert had no intention to risk losing his key midfielder and replaced him with Shea Charles, who grabbed the equaliser 12 minutes later.
Asked if he withdrew Downes to protect him from a red card, Eckert said: “Yeah. There was a little bit too much talk going on towards the fourth official.
READ: ‘I love him’ – Archer reveals who told him he would score match-winner at Swansea
“There was absolutely no necessity in the first half to make that game so chaotic. I didn’t feel that it was a particularly unfair game or a hard game.
“Then you know how it is when there are some emotions coming into the game. He was on a yellow card; he knows that.
“We know what player he is; he lives off the intensity. The only thing we needed to make sure of was that we finished with ten outfield players.”