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Hasan Abdel Fattah’s shot on the stroke of half-time ricocheted off VVV Venlo defender Yoshida into the net to give Jordan the lead before the Japanese star headed home the equaliser as the clock ticked into stoppage time.
It was a narrow escape for one of the pre-tournament favourites, who are eager to lift a record fourth continental title after losing to Saudi Arabia in the 2007 semi-finals.
“I am not satisfied with the result, especially in the first half,” said Alberto Zaccheroni, who replaced Takeshi Okada as Japan coach after the Blue Samurai reached the World Cup last-16 in South Africa in June.
“We must accelerate the speed of our play. We failed to finish on chances,” added the 57-year-old Italian.
“I expect other Asian teams will fight like Jordan. We must readjust ourselves with that in mind.”
Jordan coach Adnan Hamad said: “Our players played with confidence and a victory was possible. The result was not bad but sad.
“At the last minute, Japan managed to take points from us,” added the Iraqi, who turned Jordan’s fortunes in the middle of qualifying and guided them to their second ever Asian Cup finals.
“We should focus more on scoring as we go on.”
The Blue Samurai controlled the Group B game early on but could not penetrate Jordan’s tight defence.
In front of half-filled stands at the 12,500-seat Qatar Sports Club Stadium, they had the best of the chances with an angled shot from Borussia Dortmund rookie Shinji Kagawa punched away by Jordan keeper Amer Shafi in the 23rd minute.
Three minutes later, Yoshida found the net on the rebound off a Makoto Hasebe shot but it was ruled offside.
Jordan slowly played themselves into the game and almost drew first blood on the half-hour when Fatth trapped the ball in front of the net but his shot went straight into Eiji Kawashima’s hands.
Kagawa, who has scored eight Bundesliga goals this season, squandered another chance two minutes later when he failed to beat Shafi one-on-one.
CSKA Moscow star Keisuke Honda, who scored two goals in South Africa, was then clipped down by Jordan captain Hatem Aqel in the 43rd minute but his 30-metre free kick went too wide.
And it was Jordan who opening the scoring, with Fattah’s strike coming in the 45th minute when he picked up a cross from the left by fellow midfielder Amer Deeb just outside the box, cleverly dodged a defender and shot.
The ball bounced off Yoshida’s left foot to beat Kawashima.
Jordan almost doubled the score three minutes after the interval when striker Odai Al Saify’s header on a Deeb cross went wide.
But the Blue Samurai never gave up and fought back with Honda going close with two more free kicks.
In the 62nd minute, captain and Wolfsburg midfielder Makoto Hasebe had a decent chance when he latched onto a cross from Shinji Okazaki but his shot failed to find the back of the net.
Japan kept pressing and as the clocked ticked down and all seemed lost, they finally equalised when Yoshida powerfully headed in a cross from Hasebe to the clear relief of Zaccheroni.
Japan and Jordan are grouped with Saudi Arabia and unfancied Syria.
