The Brazilian stole the show in Rio last year but failed in all three of his attempts at 5.40m.
Making his return to competition after a month sidelined with a knee problem in Morocco his lack of form will give him major cause for concern with London looming.
Reigning double Olympic sprint champion Thompson in contrast was all smiles after annexing the 100m in a meeting record 10.87sec.
Thomspon, who owns the season's leading time of 10.71m set in Kingston last month, crossed clear of Marie-Josee Ta Lou of the Ivory Coast (10.90) in a re-run of the result in Paris on July 1.
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"My races are going fine, I'm in the shape that I want to be in and I'm looking forward to the London world championships," said Thompson.
Briton Chijindu Ujah timed 9.98sec to take the men's 100m from Ivorian Ben Youssef Meite in 10.01.
"I hope I can do something very special in London," ventured Ujah ahead of his clash with Jamaican sprint legend Usain Bolt next month.
Canada's Andre De Grasse, seen as the heir to Bolt when the Jamaican great calls it quits after London, came out on top in the 200m, timing 20.03sec.
"I was pushed in the bend but I wanted to finish strong today and to stay relaxed. I wanted to use this to tune up for the worlds, and it went pretty well," said De Grasse.
The 22-year-old made history in Rio last year when he became the first Canadian sprinter to win three medals at a single Olympics -- silver in the 200m, behind Bolt, and bronze from the 100m and 4x100m relay.
Colombia's women's Olympic triple jump champion Caterine Ibarguen gave her London prospects a confidence boost in Rabat with a leap of 14.51m to beat Jamaican Kimberly Williams (14.31m).
The Moroccan fans were served up a home 1-2-3 in the men's 1500m won by Brahim Akachab, while Botswana's Nijel Amos, who has the fastest time in the world this year, won the 800m in 1min 43.91. Kenyan Kipyegon Bett (1:44.28) came in second, with absent Olympic champion David Rudisha waiting for them in London.
Another home hope, 21-year-old Soufiane El Bakkali, saw off Kenyan rival Jairus Kipchoge Birech in the men's 3000m steeplechase in a personal best of 8min 05.12sec, and compatriot Abdelaati Iguider won the men's 3000m.
She reflected: "This was actually a training run for me. The time (49.80sec) is good but it is not very important for me now, what counts are the world championships."
With Braz flopping, the pole vault went to Poland's Pawel Wojciechowski who cleared 5.85m to beat German Raphael Holzdeppe (5.70m).
The world championships in London run from August 4 to August 13.