The 40-year-old suspect had previously been acquitted of murder charges by a district court and the court of appeals, but as Johansson's body was still missing at the time of the initial trials, both courts ruled that he could not be convicted.
However, the remains of Johansson were discovered in April 2012, leading to the man's arrest in November 2013, and a new trial that began in early January.
"This is a very clear signal that the court is very, very convinced that the man carried out this deed," Uppsala University legal professor Robert Nordh told the TT news agency.
The court ordered the man to undergo an evaluation to determine whether or not he should be sentenced to court-ordered psychiatric care.
"I'm not surprised, but I'm not satisfied," prosecutor Urban Svenkvist told the TT news agency.
The evaluation is also expected to reveal whether or not Johansson's ex-boyfriend may have "carried out the killing while under the influence of a serious mentally illness", a determination that may affect what sort of punishment he receives.
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The evaluation is expected to take several weeks to complete, at which time the sentencing phase of the appeals court trial is expected to continue. In the meantime, the man remains held on remand.
The 40-year-old suspect still denies having committed any crime.