Shares in both companies continued to slide yesterday with AG Barr down 2.5%, or 13p, to 502.5p and Britvic slipping by 7%, or 30p, to 390p.
That dragged AG Barr's market capitalisation down a further £15 million to £587m while Britvic's dropped around £50m to £950m.
On Wednesay £147m was wiped off the combined value of the businesses following the Office of Fair Trading's decision to refer the merger to the Competition Commission.
The combined group's UK market share would be around 14% compared with market leader Coca-Cola's 28%.
Analysts at Panmure Gordon said the delay, which means the takeover offer by AG Barr has now lapsed, will put Britvic in a stronger position if the terms are renegotiated.
They said: "This decision seems bewildering given the relatively small share each of these brands has of the £9 billion GB soft drinks market and the fact that Coca-Cola and private label combined account for [circa] 50% of the GB take home market.
"We believe there remains a substantial appetite among both boards to complete this merger and we are of the opinion that should the terms of the merger be renegotiated Britvic are likely to be in a stronger position."
Warren Brown, from Canaccord Genuity, said the decision was "perplexing".
He added: "We would consider that as a merged entity, Barr Britvic Soft Drinks would be able to compete more aggressively with Coca-Cola Enterprises."
Phil Carroll, from Capita, felt the OFT was incorrect in calling Barr the third-biggest player in the UK believing Red Bull, GlaxoSmithKline and Danone are all larger.
He believes the merger is still likely to go through with "minimal intervention" from the watchdog.
In a joint statement issued yesterday AG Barr and Britvic re-iterated their intention to continue trying to put a deal together even though the Competition Commission is expected to take six months to report back.
They said: "AG Barr and Britvic believe that the merger will not result in a substantial lessening of competition and that they will be able to demonstrate this to the Competition Commission.
"The boards of AG Barr and Britvic therefore intend to work together with the Competition Commission during its investigation with a view to seeking clearance of the proposed merger.
"If clearance is received from the Competition Commission on terms satisfactory to both AG Barr and Britvic, the Boards of AG Barr and Britvic will each reconsider, at that time, the terms of a possible merger between AG Barr and Britvic."
Although the companies said there was no "certainty" of a further takeover offer if clearance is received they are convinced a merger will offer benefits for both parties and add shareholder value.
Sahill Shan, analyst at N+1 Singer, said: "Ultimately, should both entities continue to pursue a merger, we are confident in our mind that the Competition Commission will rule in favour."