The County's hopes of a top two finish and the chance to compete for the County Championship title in the end of season play-offs were ended as they went down by 53 runs to the White Rose on Tuesday afternoon.
Northants were set 206 to win on the third day at Wantage Road after dismissing Yorkshire for 217, with Simon Kerrigan bowling superbly to take five for 39 from 30.2 overs, while for Yorkshire Harry Brook's 113 proved to be crucial.
The County slumped to 28 for four and 103 for eight on a wearing track before eventually being bowled out for 152, with battling lower order efforts from Luke Procter (42no), back in the side after missing day two for personal reasons, Tom Taylor (40) and Simon Kerrigan (29) not enough.
But it was the first innings effort of 170 for nine that particularly annoyed Ripley, who felt his team should have made far more of the advantage of bowling Yorkshire out for a below-par 158 all out in their first innings.
“I think the chance lost really was our first innings batting," declared Ripley.
"The wicket was a little bit better day one, and we lost guys to straight balls effectively. I think an 80 run lead was really where we should have been and would have put us in a strong position.
“Obviously when we fell short of that it was about digging in with the ball. I really felt that we did that really well. But 206 to win last innings, I still think we should win that over half (of times), I really do.
“So that's the disappointing element today, the way things didn't really go our way with the bat.
"But credit Yorkshire, Dom Bess obviously had a good game, kept us under pressure. It wasn't easy to score."
The defeat was the second close defeat to Yorkshire this season, with this loss following on from the heartbreaking one-run defeat at Headingley in May.
They are the results that ultimately cost the County the chance to finish the Group 3 campaign in the top two, which are now tied down by Yorkshire and Lancashire.
"Yeah, they have been two very tight games," said Leeds-born Ripley. "But in the grand scheme of things, very costly for us that we couldn't turn one of those into a win.”
Yorkshire skipper Steven Patterson admitted that his side had been lucky to claim two victories over Northants.
“It’s been two fantastic games of cricket against Northants, to-ing and fro-ing for both sides," he said.
"In a sense, Northants didn’t deserve to lose both games, because they played some great cricket throughout.
"When [Simon] Kerrigan came in he played beautifully, and it was starting to get a little bit nervy when we got down to 50 needed.
"You just trust you can produce enough chances over a period of time."